Revealing mistake: When the Doctor travels back in time after being shot by the stone Dalek, falls down the stairs and tells himself that he has 12 minutes to live we never see either of the 2 Doctors' faces onscreen at the same time, and if you look at the hair on the Doctor that's dying it is completely different to Matt Smith's. That's because it is Gordon Seed, Matt Smith's stunt double.
Revealing mistake: In the museum after the Doctor, Amy, young Amy and Rory escape the Stone Dalek, the Doctor uses the Vortex Manipulator to go back in time to tell Rory in 102 AD to let him out of the Pandorica. The third time he goes back, Amy moves despite being dead. (00:19:38)
Chosen answer: 1) When Stephen Moffat took over he ignored a lot of what had been developed before (there is not in-universe answer). 2) It would have killed Rose, so the Doctor absorbed the energy. His body regenerated before the energy could do a significant amount of damage that would prevent regeneration.