Theory:Doctor Who television discontinuity and plot holes/The Eleventh Hour


 * The selection of clips displayed by the Atraxi vessel includes recognizable footage from events the careful viewer knows didn't happen on Earth, or at least didn't happen on the Earth of the time in which the story is set. The opening Cybermen clip is recognizably from the moment they crashed Pete Tyler's party in Rise of the Cybermen. Likewise, there's a shot of the Vashta Nerada-controlled skeletons from The Library. There are also glimpses of Hath, who might have come to the "standard universe" Earth at some point, but not as early as the 21st century. It is unclear why the Atraxi are seeing these particular images. Perhaps it suggests they have some ability to see across parallel timelines, or indeed have some ability to look into the future. Perhaps it indicates that they have accessed UNIT computers, which might have included formal reports by Martha Jones, or Torchwood computers, which would have included information on the Cybus-created Cybermen. The inclusion of the specific image of the Vashta Narada perhaps indicates they've scanned The Library computer at some point — though, again, this would imply they have some time-travelling capabilities. It is also possible they were somehow scanning the Doctor's memories.
 * The Doctor did state that the Atraxi followed him and were "only late because he was" which suggests that the Atraxi do have at least some level of time-traveling capabilities.
 * What about the Reapers? Because they where in the alternate time line weren't they?As the Atraxi are part of the Alliance at the end of the season, they may have access to intelligence on the Doctor from other sources.


 * This is evidence for them reading the Doctor's mind or UNIT or Torchwood files, rather than scanning history (unless they have a time-space-alternate-timeline-and-parallel-universe visualiser...), but no more so than Pete's party, already mentioned in the original question.
 * It's also been established that the Atraxi is psychic because it was able to broadcast a message onto the Doctor's psychic paper. So it probably read the Doctor's mind for the images.


 * If Amy's parents never existed, then how come she is still alive?
 * While there's no definite answer here, The Doctor does state at the end of DW: Flesh and Stone that Amy can still remember the angels because she's a time traveller. He also refers to himself and River Song as time travellers being a 'complicated space-time continuim'. Amy has been living her whole life with a crack in space and time in her room -- I'm sure this can easily have a similar effect, at least enough to mean she remains alive even though her parents no longer ever existed.
 * As little sense as it makes, the cracks seem to erase just the people themselves, not the consequences of their lives, from existance. When the clerics are erased, one by one, in DW: Flesh and Stone, other clerics weren't sent in their place. A team of four clerics becomes a team of three clerics, then two, then one, then none at all. And why would the Doctor leave a team of zero clerics to guard Amy? If those clerics had their own children, their children would likely suddenly never have had a father, but they would still exist, the same way Amy still exists.


 * The prominent shot of the London Eye and the Millennium Dome in the opening sequence creates a bit of a narrative problem in dating the episode.
 * The Tardis could have travelled back in time between the 1st scene and crashing into Amy's garden.
 * The date is unknown on when The Doctor was hanging out the TARDIS. It could have been 2005 when The Doctor last left off from. If it was then The Doctor could have travelled back to 1996 because the TARDIS could have ended up anywhere after it was damaged. Although it seems unlikely the first scene is set in 2005 as it was snowing at the end of The End of Time but now it is not and there appears to be no snow on the ground. Plus, Big Ben shows it is 9:10pm but in the previous episode Rose states it has passed midnight.
 * There's precedent in the show that time-travel-capable devices set adrift will "fall through time" (and usually backward)--think of both Dalek and Victory of the Daleks.
 * Of course you'd expect that if he were travelling in a straight line (or a curve or whatever) from 2005 London to 1996 Leadworth the sky would be sort of greyish (from flashing back and forth between day and night faster than we can see) and the stars would all be streaks rather than points and so on.
 * Maybe it wasn't a straight line, but more of a zigzag path--while moving in a straight line spatially, he was mostly moving through time normally, but suddenly "fell" in time a little bit here and a little bit there (like a plane in turbulence), and it just added up to about 9 years.


 * In Amy's house, how does the Doctor know that Prisoner Zero is a multiform when he has not seen it?
 * The Atraxi may have sent more information to the Doctor's psychic paper. Or maybe he recognised the glow underneath the door?


 * The Docter has been alive for over 900 years he's probably seen plenty of them and recognized what it was right away.


 * The Atraxi looks into Amelia's room which is bright compared the prison, shouldn't it's pupil dilate?
 * Maybe they have other systems in their eyes/bodies for adjusting to different lightings, maybe their pupils only dilate for extreme changes. Or perhaps, as they are not human, what looks like pupils to us, may serve a completely different function for them.
 * Faced with bright light, the pupil should contract, not dilate.


 * In the opening scene, the TARDIS windows are clearly intact, despite having been blown out at the end of DW: The End of Time
 * They're not real windows, they're a disguise. The chameleon circuit is fixed on police box, not police box with broken windows, so the next time it materialised the windows were back.
 * it doesn't support your theory the TARDIS hurtles towards Earth right, without materialising or dematerialising so therefore the windows should be broken
 * The TARDIS is falling through time, constantly entering and exiting the Time Vortex, and therefore constantly materialising and dematerialising, thus reseting its appearance to police box.


 * If Amy has spent most of her life talking about the doctor and the TARDIS, etc., then why hasn't she come to the attention of Torchwood?
 * Who says she hasn't? Lots of people know about the Doctor—the conspiracy theorist from Rose, the LINDA club, etc.—but apart from a notation in the Torchwood files they seem to be left alone.
 * She didn't remember the Daleks or why there were no ducks in the duck pond. There is a very good chance the same reason applies to Torchwood.


 * In the rooftop scene in the hospital, when they step onto the roof the doctor is carrying/wearing various ties, but he has neither the red bow tie or tweed jacket which he is wearing at the end of the scene with him.
 * Rory is carrying a tweed jacket underneath a red one. However at the end of that scene Rory is still carrying a tweed jacket (although the doctor has one on) and the red jacket has disappeared


 * The Doctor has to use a really complicated method to point the Atraxi to Prisoner Zero. But after Prisoner Zero is beamed away, he is suddenly capable of phoning them and complaining about their intent to burn Earth by invoking the Shadow Proclamation. Why didn't he do that in the first place?
 * The Doctor clearly states that he is tracking the signal back to the Atraxi.


 * The Doctor asks Amy how long it has been since Amelia has lived there. Amy replies six months. Then when the Doctor tastes the shed he says he's 12 years late. Surely he would know that it could have been 11 years and six months until Amelia moved, why suddenly accuse Amy of lying to him?
 * He knows he's 12 years late. He's not necessarily sure that Amy's lying to him. In fact, he's a bit confused, and trying to work things out in his mind. And, as we know from later episodes, 11 can be pretty rude while he's doing that. It's only after he says, "This matters. This is important. Why did you say six months?" and she replies, "Why did you say five minutes?" that he figures it out.


 * When the TARDIS first appears on screen in this episode, the lamp on top (materialisation beacon) does not flash. But when we see the first wide-shot with the Doctor clinging to the TARDIS the lamp does flash.
 * There is sufficient time in between the shots for the light to begin flashing and is likely to not have been working properly as the TARDIS was broken at the time.


 * After the TARDIS flies over the Big Ben, the door sign is on the right door (not the left one).
 * No it isn't.


 * At the end of The End of Time the Eleventh Doctor is wearing the Tenth Doctor's suit jacket, and at the start of The Eleventh Hour he is not. Why?
 * Because a large amount of time may have passed, and with fire everywhere, it would be hot.


 * Rory has spent months photographing the coma patients walking the streets, he has pictures of all of them, which The Doctor uses to send to the Atraxi. Why then doesn't he notice that the woman with the two children talking to them when they return to the hospital is in fact a coma patient?
 * It is possible this disguise was the wife and kids (or some other relations) of a coma patient. The Doctor did say that whatever a coma patient dreamed of Prisoner Zero takes on that form.
 * It is not a relation of the coma patient. You see her as one of the coma patients.
 * Rory may not simply spend enough time with the patients to register immediately that it was one of them.


 * No responsible parent or caregiver would let a child that young use an oven unsupervised.

It's been pointed out throughout the series that Amy's parents weren't around for "some reason", made obvious in The Big Bang. Also, Amelia's already said by this point that her aunt, who supposedly cares for her, isn't in the house. So perhaps it's just a case of irresponsible aunt?
 * Young Amelia is Right-handed and has blue eyes. Grown Amy is left-handed (although Karen Gillan is right-handed) and has brown eyes.
 * Eye colour can change during puberty (on rare occasions) and hand-favour can be changed with some mental training. Also, some people are equally skilled with both hands, which could possibly be the case with Amy.


 * On the rooftop, how does the Doctor magically produce a TARDIS key from the pocket of a tweed jacket he literally just obtained?
 * The key materialises in his pocket. You can clearly hear the materialising sound just before the Doctor reaches into his pocket to grab the key.


 * The TARDIS has its own gravity, according to the Doctor in Journey to the Centre of the TARDIS (TV story), so why did he need a rope to get to places in the TARDIS?
 * The gravity systems may have been undamaged in Journey to the Centre of the TARDIS.


 * If getting hit by a bat made him better, why wasn't he better when he was hit by the tree?
 * Blunt force doesn't always have the same effect on a body.


 * How does the tardis key materialises by itself in the Doctors jacket?
 * A tardis has self awarness it could have send it to the Doctor


 * How could Amelia understand Atraxi's word "Prisoner Zero has escaped" even before the Doctor and TARDIS appear? Surely Atraxi wouldn't use English as their native language.