Continuity mistake: When Rory brings the unconscious Amy inside the TARDIS and puts her on the floor, the Doctor drapes his jacket over her twice. (00:39:44)
Continuity mistake: When Purcell is sinking into his carpet, just after a shot where he's shown having sunk into the floor up to his waist, we see a shot focusing on his dog where Purcell's legs are visible as he falls forward onto his hands, despite his legs having already been pulled under. (00:23:38)
Continuity mistake: When the Doctor is talking to the Voice Interface Amelia, when he starts saying that "Scotland's never conquered anywhere, you know, not even a Shetland", his left arm, which was stretched out along the railing in the previous shot, is suddenly lowered. (00:27:28)
Revealing mistake: When River grabs a gun off one of the soldiers she just knocked out with regeneration energy, the actor sits up slightly, even though the soldier is supposed to be unconscious. (00:24:44)
Continuity mistake: When the Doctor is talking to the Amelia voice interface, in a shot of him from behind his position slumped against the railing is different from shots of him from the front. (00:27:37)
Continuity mistake: When the Doctor is watching Jimmy and Adam at the end, his hands go from clasped in front of him to tucked in his pockets between the wide shot and the close-up. (00:40:37)
Continuity mistake: After Rory receives the telepathic message, when he tells Amy what happened, his left hand jumps between rungs of the ladder he's climbing. (00:30:20)
Continuity mistake: When Idris/TARDIS tells the Doctor he's like a kid trying to rebuild a motorbike who never reads directions, her arms change position and the circuitboard she's holding switches hands between a close-up and following wide shot. (00:23:41)
Audio problem: When Idris/TARDIS says to the Doctor "And you don't care that it's impossible", in a shot from behind them her jaw does not move as she speaks. (00:22:49)
Continuity mistake: When Idris/TARDIS starts to run out of the room only to stop, grunt in pain and put her hand to her side, the hand in question switches from her right to her left between shots. (00:20:41)
Continuity mistake: When Idris reveals she's the TARDIS and the Doctor disbelieves it, her right hand moves between shots while it's resting on the bars of her cell. (00:16:32)
The Curse of the Black Spot - S6-E4
Continuity mistake: When the Doctor is telling Amy that they have to release the Siren, his hands on her collar change position between shots. (00:30:05)
The Curse of the Black Spot - S6-E4
Continuity mistake: As the Doctor explains that the TARDIS is headed for a "full-on screaming tantrum", the lever his right hand is on moves between shots, and he's not shown pulling it. (00:18:40)
The Curse of the Black Spot - S6-E4
Continuity mistake: When the pirate whose hand Toby cut pulls his gun on the kid while Toby is pointing a sword at him, when Mulligan grabs the keys from the other man's belt, the positions of the weapons change relative to each other. (00:18:20)
The Curse of the Black Spot - S6-E4
Continuity mistake: When the TARDIS starts shaking ominously while the Doctor and Captain Avery are onboard, the handle of the big starting lever on the console moves between shots. (00:18:03)
Continuity mistake: When the orphanage director is wiping at the writing on the wall before leading Amy and Canton onward, the cloth jumps from his right hand to his left hand and back. (00:12:54)
Revealing mistake: When the girl raises her visor to reveal herself in the spacesuit, the cracks in the visor from where it was shot earlier are drawn on. (00:20:22)
The Impossible Astronaut - S6-E2
Continuity mistake: When the Doctor goes to take off the spacesuit helmet, his hands change position between shots. (00:32:53)
The Impossible Astronaut - S6-E2
Continuity mistake: When the Doctor asks Rory if everyone's cross with him for some reason, his left arm moves from by his side in a close-up shot of him to stretched out to the console in a shot from behind. (00:15:06)
Continuity mistake: In the mini-episode "Time", when the Amys start flirting and the Doctor quips about it, Present Amy's hand goes from resting on the handle of the TARDIS door to lowered between shots. (00:01:09)
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.