Theory:Doctor Who television discontinuity and plot holes/The Name of the Doctor


 * Why couldn't the Great Intelligence just go back in time and kill the first Doctor when he was born, as opposed to making him lose every battle throughout his life?
 * Who's to say he can't? What is worse, removing him from existence, or undoing and destroying every part of him over and over again? Don't forget the Great Inteligence is sadistic and wants revenge.
 * The Great Intelligence seemed to make his purposes pretty clear, however given the circumstances it may be that it is very likely that he was fully aware that the paradox that would be created in trying that would be too great to consider.
 * We don't know if he tried, but a Clara was there to stop him. Though, as noted, undoing all the good the Doctor did in his life more closely fits the G.I's modus operandi.


 * At no time is it made remotely clear how The Great Intelligence travels to Trenzalore with his hostages or how he travels through time (which he clearly has if he remembers all of his thwarts by The Doctor, and knows so much about other things, in 1894!). Clearly, at some point, he must have picked up on some of the same secrets the likes of Lady Peinforte did...
 * The Great Intelligence is an incredibly powerful being, a creature that is an old one, and this as he makes it clear is chronologically his last appearance, and he is clearly from somewhere in far future. Evidentially in all that time its found a way to unlock even greater powers than before, for such a strong being is that so unlikely?


 * They pretty clearly state that "time travel has always been possible in dreams". And, we know that the GI exists on the "astral plane". Sounds like it'd be pretty easy for him to have learned about the future.


 * He believes it will be his last appearance Clara seemed to believe the same about herself but it turns out that may not be the case. Whether it really is his last appearance will depend on what later writers want to do later.


 * If the "John Hurt" Doctor is the Doctor's future, how does he know about him?
 * Because he's not the Doctor's future, he's his past.
 * How do we know he's from his past ? Maybe he met his older-self ?
 * They really haven't yet told us whether he's from the future or past, so while speculating may be fun, it really can't be claimed as a discontinuity at this point.
 * The Doctor calls him the "one who broke the promise", the unplaced Doctor defend "what [he] did", the use of the past tense suggests an older incarnation.
 * Given the absence of any other future Doctors, it can be assumed that the unknown Doctor is from the past.
 * And you know what happens when you "assume"... Most likely, it is indeed a here-to-fore "missing" incarnation, but we don't know that yet. If it is, then that easily answers the question of how the 11th knew him. If it's a future incarnation, then I expect it will be explained in the next episode. Either way, there's no plot hole/discontinuity to be discussed here at this point.
 * This is perfectly consistent with almost every multi-Doctor story ever (the only exception I can think of is "Time Crash"), including the various "pseudo-multi-Doctor" stories in the novels, where one of the Doctors knows more about his future incarnations than he seems to have reason to, and the reason is never explained.
 * Also, there are many ways this could easily be explained in the following episode. If he's an Eight-and-a-Halfth Doctor, he's not in the Eleventh Doctor's future. If he's the Valeyard, it makes perfect sense for the Eleventh Doctor to know about him despite being in his future. And so on. The fact that they don't tell us which of the many possibilities is the case is not a discontinuity, unless every cliffhanger ever was a discontinuity.


 * The Doctor states he never learned about his tomb, so how does he know so much about it when he gets there?
 * Because his tomb is the TARDIS, and he know lots about the TARDIS.
 * The Doctor appears able to describe the circumstances of his death and why he is "buried" there. This is more likely to have been what the original poster was referring to.
 * At no point in the episode is it ever stated how the Doctor dies. There's no indication the Doctor knows (or wants to know) how he died. Some guesses involving battles are stated, and the Great Intelligence appears to know. But the Doctor himself gives no clue other than knowing the location.
 * OK, perhaps. But I hope you will allow for the misunderstanding given the esteem the audience is expected to hold the Doctor and what he says in.


 * Where is the Ninth Doctor? He doesn't appear, yet Clara stated she saw all the doctors?
 * Clara saw and saved all the Doctors, so she must have encountered 9 off-screen.
 * There was apparently thousands of Claras that we didn't see, but the 9th is actually one of the doctors walking past her in the mist so he is represented in the episode.
 * The Ninth Doctor runs past Clara when she is in the Doctor's timestream (look for the leather jacket). Clara's interactions with him otherwise occur off-screen.


 * How did this episode connect to the prophecy and the work of the Silence? The Doctor left Tranzelore without actually answering the question and nothing seem to have changed as a consequence of it.
 * That is yet to be seen. What we see in this ep is the aftermath of that.


 * The Question was asked on the fields of Trenzalore, at the fall of the eleventh, just as the prophecy said it would be. It's just that River ended up being the one who answered it instead of the Doctor (who, you'll note, isn't specified as being the person to answer it in the prophecy; in fact, the prophecy doesn't mention anyone in particular, it just warns that the Question must "never be answered"). The Silence's connection to all of this is that they took the prophecy's warning to heart and became determined to ensure that, since they believed the Doctor was the only one who could answer the Question, his silence would fall when the Question was asked by killing him before he could get to Trenzalore. So basically, the events go like this: The Silence learn of the prophecy and decide that they must kill the Doctor in order to prevent the Question from being answered > the Doctor tricks them into thinking that they succeeded by using a Teselecta to fake his death > the Doctor, still living, is drawn to Trenzalore by the Great Intelligence who asks the Question that the prophecy warns about > River answers the Question instead of the Doctor, and the Doctor's tomb opens. Although it is good to point out that the Doctor has not yet left Trenzalore, or even his own timestream, for that matter.


 * Stephan Moffat is incredible. In this episode he had Clarence DeMarco declare that "The Doctor has a secret...he will take to his grave; and it is discovered. The grammatical error is obvious but people do sometimes do that. In this case, however, the statement turns out not to mean what that allowance suggests it means and Stephan Moffat is able to have the doctor accuse Clara of not listening and then pull the rug from under everyone by revealing that that allowance is deceptive.
 * When people try to explain the prophecy in reference to what we see in this episode it feels like they haven't been listening either. Now it's unclear what the prophecy actually is because "Silence will/shall/must fall when the question is asked." isn't the prophecy; it's the Silence's belief system that the answer to the question must be prevented from being articulated and, unless there's some miracle, by the time he reaches the point when the question is asked of him it will be too late.
 * Why? Dorian told us: "On the fields of Trenzalore, at the fall of the eleventh, when no creature can speak falsely or fail to answer, you will be asked a question..."
 * At the top of this response I remarked that SM was tricky and clever with language but at the moment claiming River won't cut it. Dorian suggested an imperative. Some event or agency that compels truth and frowardness. When asked the question is asked the Doctor would elect to lie, on Trenzalore he can't. When asked the question the doctor would choose to try to avoid it, at the fall of the eleventh, he can't. It was the compulsion Dorian described that scared him into considering letting the Silence kill him and unless you can explain those three words in relation to what happens in this episode then you can't claim the prophecy is fulfilled.
 * The truth-compelling factor at Trenzalore could be the Great Intelligence using the Whispermen to kill the Doctor's friends. By doing that, he's pressuring the Doctor into answering (so he can't fail to answer unless he is willing to let his friends die, which we know he isn't), but the Doctor can't lie his way out of it because there is only one correct answer that will open the tomb; any other answer he gives won't open it.
 * It seems pretty clear that the Silence were right all along. When the Great Intelligence entered the Doctor's timeline, it wasn't just Jenny's life and Strax's new circumstances that vanished; the stars began going out. That's what they didn't want to happen. And if River had successfully killed the Doctor, it wouldn't have happened. The fact that it turned out to be River, rather than the Doctor, who spoke his name is a cute little twist, but it isn't actually relevant; she wouldn't have been there either if she'd killed him.
 * Again (two posts above) that ignores what Dorium said which was that "no creature" could speak falsely or fail to answer. That phrase includes everyone and excludes no one. It means the Doctor, Clara even the Great Intelligence would be compelled to tell the truth in the circumstances created by the fall of the eleventh. The circumstances Dorium described aren't particular to the Doctor, they're just particularly unfortunate for him because they make it impossible for him to keep his secret.
 * This may or may not have been the fulfillment of the prophecy, and to be honest I'm not really invested in it either way. I suspect time will tell. However, one can certainly argue that this incident does indeed fulfill it. Dorium was speaking poetically, probably recalling something he had previously heard elsewhere himself. For example, he calls it "the fall of the eleventh", rather than saying "when you die". His mildly poetic use of "when no creature can speak falsely or fail to answer" is absolutely met by this circumstance. "No creature" could lie or fail to answer if place in the Doctor's situation, without losing in one way or another. If he fails to answer, the GI kills his friends in front of him. If he lies, the GI will know, as the door simply won't open. It's a very well-done trap that he doesn't really have a way out of on his own. The Doctor is compelled to either give up his secret and let the GI access his timestream, or watch his friends die. As it happens. he lucks out, because the GI didn't know that River was "virtually" there and able to communicateb his name nice and silently to the TARDIS. (And of course he wouldnt really have cared, he just wanted to the door open.) So again, it might be that they have something else in store on Trenzalore, but it's not necessary in order to fulfill the previously-stated prophecy.


 * We see several TARDISes on Gallifrey, all still in their default shape, which is shown here to be a cylinder. Hasn't it been established that the default TARDIS shape is a cube? Or am I just misremembering?
 * We've seen cubical SIDRATs. And what may have been a TARDIS or a SIDRAT, but it's debatable.
 * SIDRATs were just imitation TARDISs, same functions and potential, just limited lifespan as they were designed to be operated by remote control. There's no little reason to assume they should have different form.
 * In fairness to the point, yes, those were indeed TARDISes in cube shape that we saw near the end of The War Games, as well as the SIDRATs from earlier. However, the fact that those ones were in cube shape, while some other group of TARDISes from many, many years earlier were in a cylindrical shape in this episode, really doesn't seem like a problem. Maybe different TARDIS models have different default shapes, or maybe protocols say that ones in for repairs go to cylinder instead of cube. Or maybe it was just the "in thing" later on Gallifrey to default them to cubes. Again, it seems like a pretty minor difference, given that we know how trivially easy it is for these things to change forms.
 * Such as cars on Earth. Modern cars look different to the first cars in many ways, but the prinicple shape remains the same.  The TARDISes on Gallifrey keep the same piller form, but a different shape.
 * It's long been established that the Doctor's TARDIS was an obsolete model, so maybe the old ones were cylindrical.


 * How, exactly, did the Doctor enter the timestream of his entire life without it collapsing?
 * It was collapsing, he simply got out before it collapsed, once he left it stopped, think of it like climbing into a sinking ship, and then out before its completely submerged.


 * If Clara split into a hundred pieces (or some number) how did the Doctor extract "his" Clara? How was she still in tact? How would he even find her?
 * What he took out, was the last true Clara, after being split her original essence, hit the bottom. Don't forgot this is the doctors personal history were talking about, he would obviously know where she was.


 * A related question: How could Clara give that speech at the beginning of the episode, in which she isn't sure where she is, but is aware of living many many lives, and of her overarching intention to save the Doctor? Each individual Clara would only be aware of their own individual life, so the Clara that gives this speech would have to be some transcending "original essence" as postulated above. BUT this is clearly contradicted by River's comment when Clara is considering entering the Doctor's timeline: "They won't be you; the real you will die; they'll just be copies". River is too smart and knowledgable to plausibly be wrong about this, and would have no plausible motivation for lying.
 * The Clara that gives the speech is the original Clara, and she is still in the process of being "broken into a million pieces." She can feel it happening; she is becoming more aware of the lives that her copies led while her own mind and memory is disintegrating, which is why she doesn't know where she is and why she can only remember that she has to save the Doctor.
 * But River is wrong, and she acknowledges this later in the episode when she tells the Doctor that if Clara was dead, there couldn't be a mental link still functioning. So River didn't lie -- she was simply wrong. It all ties into the theme of Clara being "the impossible girl."


 * How could Clara, a human being, undo the acts of the Great Intelligence throughout all of the Doctor's incarnations? This is implied in the episode synopsis. I mean, the Doctor himself had great trouble defeating the Great Intelligence in the past. How would an inexperienced human being undo what the GI had done (that had affected people's existence or the removal of galaxy's.
 * The GI went back and made small changes so as to destroy the Doctor. All Clara had to do was undo the small changes that he made. We saw her save the Doctor as "an inexperienced human" in Victorian London and in the Dalek Asylum. Besides, one of the Doctor's over-riding commentary on humans is it's that they can be pretty resourceful.
 * It is also stated that the GI dies as a result of his interference, so Clara likely never had to encounter him directly, just undo what he did.
 * In Interference, the Doctor specifically said that it would be easy for someone else to undo Faction Paradox's changes to his timeline, it's only difficult for him to do so himself, because that would cause further corruption. (In the FP novels, that's even given as part of the reason Cousins kill their own parents before anyone else can, but those aren't canon on this site.)
 * We don't know if all the Claras were human. For example, it's assumed the Clara the First Doctor meets on Gallifrey is Gallifreyan (two hearts and everything). Similarly, the sequence with the Fourth Doctor is taken from The Invasion of Time, also set on Gallifrey, so that version of Clara might be another Time Lord version (or perhaps even the same woman who helped the First Doctor). We already know one of the Claras was technically a Dalek; for all we know there might have been a Cyberman who helped the Doctor behind the scenes who was a converted Clara. There is precedent - see how converted Yvonne Hartman was still able to fight the Cybermen in TV: Doomsday; indeed, we don't know for certain that every Clara looked identical - for all we know Yvonne could have been a Clara, setting herself up to help the Doctor once converted.


 * Was Clara literally born over and over again in each part of the Doctor's timeline? The shot of her as a child in Victorian London certainly seems to suggest so, but it seems extremely unlikely that if that were really the case, she could grow up, learn about who the Doctor was, learn about the Great Intelligence and what he was doing to the Doctor, and in some cases, become a companion of the Doctor (who we never saw or heard of) so that she could be on-board his TARDIS is the right times. And if she was reborn every time, does that make the version of he on Gallifrey a Time Lady? Furthermore, if she was reborn each time, then how? Did she just suddenly appear as a fetus in random women's wombs? Surely her whole family tree wouldn't have been split with her (as that would endlessly multiply the world's population forever), so her specific parents wouldn't have been split across time in addition to her (which causes more questions about her being born to people whose traits didn't match her own and so on; what if she were born to an Asian couple or something like that? Since we know that she was on other worlds as well, what happens if she's born to a Slitheen couple on Raxicoricofallapatorius?). Did she just appear as a baby out of nowhere?
 * How exactly splitting ones self across time lines works is by no means explained. But considering that is its, by no means should it resolve any of these errors, it simply implants Clara in random places across the doctors time steam, there she grows up, and either remembers as she got older or simply subconsciously knew. Presumably to minimalize paradoxes she would only appear in the places which would cause the least of these errors, after all the doctor states changing history has a way of working itself out. And why shouldn't she be born every time to a Caucasian humanoid kind, after all there are billions out there (just watch every episode of the classic series for proof).
 * There is a slight hint given that while WE see Clara, the Doctor might have seen her as someone else. For example, note she is dressed similarly to Jo Grant when she yells at the Doctor driving Bessie; perhaps he saw her as Jo Grant in that moment. The fact the Doctor likely saw someone else's face is supported by the fact the Eleventh Doctor didn't recognize Clara despite having met her face to face on Gallifrey during his first incarnation.
 * The Doctor saw her for 5 seconds on Gallifrey ~1000 years ago (subjective to him). Do not expect him to remember her face.
 * But there are have been many occasions throughout the show's history where the Doctor has remembered just such an encounter. Plus, frankly, one would expect the Doctor to remember that a young woman suggested he take the TARDIS he's travelled in for 700+ years. It's not something one would forget, as opposed to, say, some random woman yelling at him has he drives by in Bessie.
 * Neither City of Death nor Set Piece explains how a being that's splintered through time ends up with identical-appearing copies in various time zones. (IIRC, the Doctor explicitly tells Benny that he'll "explain later" about the bartender, but never does.) How is it a problem that the same thing happens to yet another person in another story?
 * On the other hand, he also very casually forgets things sometimes - such as not quite recognizing the name Great Intelligence when he's in Victorian London. As he was stealing a TARDIS, he was about to run away and make a huge and no doubt frightening change in his and his granddaughter's lives. He probably wasn't focused on recalling in detail the face of a random technician whom he met for a few seconds and who pointed him to a different TARDIS. And even if he had, the ensuing adventures he was about to have (and keep having) were likely more than enough to distract him from recalling the details for long.
 * For the purposes of storytelling, we see the same actress, but that doesn't mean Clara always had the same face. Aside from the First Doctor's encounter, note that the Third Doctor clearly sees her in Bessie's mirror (and probably stopped to ask why she was shouting at him).
 * Alternately, as "time can be rewritten" it's possible that the Doctor, post-Name of the Doctor, does indeed now possess memories of encountering Claras throughout his history. But he didn't before. Timey-wimey and all that, right?


 * How did Clara know which TARDIS to pick? They all looked identical, and she's only ever seen the Doctor's TARDIS in its police box shape. There was nothing outwardly remarkable about the one that she was standing next to.
 * Every Clara had their own life. So this Clara was a Time Lord, she may have been a technician and knew what TARDIS had the broken navigational system.
 * In The Doctor's Wife we learn the TARDIS orchestrated the Doctor stealing her. Presumably she was in cahoots with Clara. If she (the TARDIS) exists across all time and space, as stated in Doctor's Wife, it's even possible she was perfectly aware of Clara's mission, hence her apparent distrust of Clara.
 * If Clara is the one who introduced The Doctor to His Tardis, than why is it so distrustful of her?
 * Exactly how sapient and aware the Tardis is is unclear, it rages from completely to not at all. As such is probable it had no way of knowing Clara was responsible. And distrusted her as it could sense something was wrong with her (her destiny to become fractured).
 * The TARDIS's later distrust is clearly implied to be due to Clara's special status.


 * How exactly did Oswin and Victorian Clara stop the Great Intelligence in "Asylum of the Daleks" and "The Snowmen" (and by that, I mean the "current" Great Intelligence who entered the Doctor's timeline on Trenzalore, not the one who had just contacted Simeon for the first time), respectively? We see Claras in both of those stories, but there is no hint of the Great Intelligence's interference, and we don't see the Claras doing anything to undo the Great Intelligence's alterations; she's just there, almost as if from the moment she walked into the timeline, the Great Intelligence became completely irrelevant to what she was doing.
 * Maybe she did, or maybe those were just other times a version of her saved the Doctor. We do know from Madame Vastra that at some point after the GI went back that the Doctor would have died in Victorian London and the Dalek Asylum. Maybe some of the events we saw actually were influenced by him. For example, in Snowmen the Doctor seems to have Simeon defeated, then is shocked when the tables turn and the GI suddenly has control, until Clara saves the day (by dying, in that case).
 * We don't know the extent of Clara's interference. For example, all she had to do with the First Doctor was point him to the right TARDIS. Not all her fixes were necessarily coming in with guns blazing. Google "butterfly effect" and you'll see that, sometimes, just her presence was enough. For example, she shouts at the Doctor driving Bessie, causing him to slow down ... so he's properly aligned to be time-scooped to the Death Zone and TV: The Five Doctors.


 * Why do all of the other Claras appear to know about the Doctor (to the point where they recognize him and shout his name), whereas Oswin and Victorian Clara don't have any memory of him?
 * Oswin and Victorian Clara were likely just pretending to not know him. I mean, think about it: if they ran up to him and said "Hello Doctor, I'm a future companion of yours who jumped into your timestream to stop the Great Intelligence from killing you thousands of times over," would he really believe them?
 * Alternatively they genuinely didn't know, but subconsciously remembered what they were supposed to do.
 * This is what the episode appears to imply. She was given the instincts but otherwise has no knowledge as to why.
 * We also don't know the backgrounds of these Claras; each one may have spent years studying the Doctor, whereas the circumstances for the Asylum and Snowmen Claras might have just dropped her into his lap.


 * If the Doctor never notices Clara, then how does she actually save him from the Great Intelligence? She seems to be trying to get his attention so that she can alert him of the Great Intelligence's interference, but he almost never hears her. Most of the Doctor's life should still be corrupted.
 * Why would he need to know she's there in order to be saved by her? There's no indication that's necessary.
 * The episode never goes into detail to explain how the GI interfered, so there's no need to go into detail as to how Clara potentially fixed things, or for that matter if she was always successful.
 * And what detail the episode _does_ give us tells us that she wasn't even _supposed_ to succeed in every case. One of the first deaths they mention is Androzani, and if she'd saved him there, that would have been a problem…
 * As just a small point, we don't know for certain that the death on Androzani that Vastra mentions is referring to - it could be his fifth regeneration as we've seen before, or it could be that the GI prevented him from doing so, and hence he really died rather than regenerating. Or it could have been a completely different time he was on Androzani (Major or Minor). Regardless, the explanations above still hold that he didn't necessarily need to have noticed her every time for her to sufficiently save him from the GI's interference.


 * Why exactly is it a paradox for the Doctor to visit his own grave? I mean, obviously standing over one's own dead corpse is in itself a contradiction, but should't time travel make things like that possible? What makes it dangerous?
 * I don't think simply going to his grave would create a paradox, but it does put him at a high risk for doing something that will create one (especially since there's a physical manifestation of his entire timeline on Trenzalore). That's probably why the TARDIS resisted, and the Doctor was likely just speaking generally about it being a really bad idea.
 * The novels do explain this to some extent. Of course they also have the Doctor averting the problem (Alien Bodies ends with him burying his own future corpse). And it's not clear whether Moffat meant this case to be similar to the cases in the novels, or whether the "timestream" we saw was the same thing as the "biodata" invoked in the novels' explanations.
 * Well, if it's not the same thing… then it's something else that hasn't been explained, which would presumably be obvious if you understood Gallifreyan temporal physics but isn't obvious to us primitive humans. The show is full of such cases. How does the Blinovitch Effect work? Why does the TARDIS care that Jack is a fixed point in time and try to keep him out? How is any of this a problem? If the Doctor hadn't told us there were a problem in advance, that would be sloppy storytelling, but the Doctor not explaining the physics is not.
 * The idea of the Doctor never seeing his grave is a bookend to the Ponds in The Angels Take Manhattan in which it is explained that, while time can be rewritten, there are occasions where learning certain information -- such as finding one's own grave -- locks things into a fixed point in time. By acknowledging and visiting his gravesite, the Doctor is concerned he may now have locked his eventual death into a fixed point. If his grave was in London, the same would occur if he were to stumble across is, though without the knowledge, London, or Trenzalore, would just be another place.


 * We were looking at Doctor's entire timestream. So why there were no future incarnations there? This suggests, that the 11th is the last one. (Or the "unknown" will be 12th and the last one.)
 * Or simply that we weren't shown any future ones. We also didn't see all of the variations of Claras out there, only a small selection.
 * Is it possible that the future Doctors were hiding? The Doctor is a clever man, and his future selves might have hidden from sight to make sure no paradoxes ensure.  The Hurt Doctor seems to appear from nowhere, so the futures might have done the same.
 * This is another one of those things that's partially explained in the novels, at least if you assume that the timestream is somehow closely related to the notion of biodata in the novels. The Doctor is literally unable to see his own future unless it's explicitly pointed out to him, in the exact same way that humans are unable to see alternate strands of the past unless pointed out. There's no reason to believe that's any different from inside the timestream than from outside.
 * Also, in the various stories where the Doctor has been inside his own head/peeked into the timestream/etc., the future Doctors have always been shadowy and indistinct at best. In the NA novels, they were behind doors that hadn't been opened yet. And when the 6th Doctor is forced to see the 7th, it's apparently both surprising and painful to him.
 * Alternatively… unless Clara manages to fix the Doctor's timestream, and the Doctor manages to get back out of his timestream—which hasn't happened yet—there can't be any future Doctors. As history stands right now, the 11th Doctor is the last. Once they succeed, his future incarnations will come (back) into being.


 * How might the Doctor and Clara have survived the fall from Trenzalore's atmosphere to its surface inside the TARDIS? If the TARDIS' outer shell was damaged, it must have been a rough landing.
 * The inside of the TARDIS is another dimension that (typically) isn't affected by things that tamper with or damage the outer shell. While it probably was a bit of a rough ride due to most of the TARDIS' precautionary systems having shut down, they would have been relatively safe inside of the ship


 * Could the momentous disaster the Unknown Doctor is responsible for be the use of the Moment to end the Last Great Time War? Maybe the Doctor couldn't kill his own people, so he went to his last incarnation, who was at the end of his life and had nothing to lose. The Unknown Doctor said that what he did was for peace and sanity. What better threat for peace and sanity than the Last Great Time War?
 * Quite possibly, but this isn't a page for speculating future events, its for reporting and discussing errors.


 * Wasn't the TARDIS at a museum, not a repair shop, when he stole it?
 * Nope its been established it was in the repair shop since at least tom bakers reign, although other time lords often stated it belonged in a museum, it was never put in one.
 * Although we've occasionally heard the TARDIS referred to as a "museum piece", it's doubtful that was meant literally. It's just a term meaning that it was already out-of-date even when the Doctor stole her.
 * Many museums have maintenance shops for maintaining or preparing exhibits.
 * And again, noone has ever implied that the TARDIS was literally a museum exhibit. It's simply a term referring to it as having been already obsolete from the beginning. The Doctor has clearly stated more than once that it was "in for repairs" when he stole it.


 * In The Brilliant Book 2012, it is stated that The Doctor saved Vastra from being a savage, primal Silurian. So why didn't she revert back to that Vastra in the episode?
 * The Brilliant Book not being an authoritative source, it may have been wrong. Regardless of that though, the changes to people and time lines seem to have been happening gradually. Jenny didn't disappear right away, Strax didn't revert to a different persona right away, stars were not all disappearing at the same time, etc. Vastra might very well have been affected eventually, if the damage hadn't been undone.
 * The revival-era Silurians have never been depicted as "primal" or "savage" but intelligent beings with science and medicine. While Strax underwent personality changes over years of being exposed to Vastra and Jenny, the Doctor, and serving as a nurse, Vastra was simply angry and out for revenge when she was discovered. Her true personality might have been a peaceful one and therefore she was less likely to suddenly revert into something that might have been a danger to Clara.


 * The doctor only met Present Clara because he had already met her future fractured selves, but she only fractured because she met the doctor, doesn't that make the whole thing on great paradox.
 * Nope. Just a causal loop. Similar things have happened several times, such as the Tenth Doctor only knowing what to do in Time Crash because the Fifth Doctor saw the Tenth Doctor doing what he remembered.


 * How is it that at the beggining of the episode the technician says "a TARDIS has been stolen" if it's the Doctor's grandaughter who names the TARDIS "TARDIS" after she's already travelling in it with her grandfather, I mean, the TARDIS is not "the TARDIS" yet, if you know what I mean...
 * Susan said that she came up with the name herself, but we don't know that it was after she left Gallifrey. She may have indeed coined the phrase (after all, why would she lie?), but it may have been long before the Doctor took her with him when he stole one. We don't know how prominent in Time Lord society he or she were before that, but it may have been enough to get the term in common usage.