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


 * Why was Clara fine after hanging on to the TARDIS in the vortex? Captain Jack died!
 * The Doctor specifically noted that the Tardis extended the shields to cover her. Given that it was trying to shake Jack off during his trip, while she's the one who saved the Tardis' Doctor throughout his whole timeline, it's understandable that she'd be treated differently.
 * How could the Doctor lie about having a plan at the end of the episode? --  Ransom Time 
 * Technically, he didn't say what kind of plan he had, or which situation it may pertain to. His comment about not having a plan to Clara was to clarify he didn't have a plan for what she thought he meant. Also, moments later he reminds Clara that they already supposedly saw what happens here, so they can't change it. It's likely that he did have a plan of sorts- to die. Or in contrast, perhaps his plan was to "talk very fast, hope something good happens, take the credit".
 * The Doctor is on his last life, so why did the Teselector have to imitate his regeneration in The Impossible Astronaut, it would have been believable enough if he just died as he had no remaining regenerations.
 * Perhaps the doctor didn't realise he was on his last life until he realised that he had lived significantly longer than all his other incarnations and then put 2 and 2 together and came to the conclusion that 10 had used two regenerations, resulting in the eleventh doctor being the thirteenth incarnation.
 * Why did he ask the TARDIS if he could regenerate after being poisoned in Let's Kill Hitler? Even though the poison prevents regeneration, he doesn't have any regenerations remaining anyway!
 * Perhaps the doctor didn't realise he was on his last life until he realised that he had lived significantly longer than all his other incarnations and then put 2 and 2 together and came to the conclusion that 10 had used two regenerations, resulting in the eleventh doctor being the thirteenth incarnation. This would also explain why the TARDIS says that regeneration is disabled.