The Impossible Astronaut - S6-E2
Continuity mistake: When the alien kills Joy in the bathroom in front of Amy, the fragments of her body disappear from the floor once the alien approaches Amy. (00:28:28)
A Good Man Goes to War - S6-E8
Continuity mistake: Rory threatens Madame Kovarian with a sword. It's on her neck, then in the next shot the sword is not touching her. (00:23:38)
The Impossible Astronaut - S6-E2
Continuity mistake: When the Doctor is shot and killed while trying to regenerate on the beach, he falls with both legs extended. When River, Amy and Rory run up to him his left leg is bent. The camera cuts away again, and when it cuts back to show the Doctor's body one more time both legs are straight again. In addition, his left arm changes position between shots, between stretched out pointing away from his body on close-ups to bent with his hand resting on his thigh in wider shots. (00:08:15)
Continuity mistake: As Lucy goes down the hall, she opens door 214, then 215. As she comes to the next door on the right, she opens 214 again, rather than it being 216. This is particularly noticeable because the third room she enters is "her" room, containing her greatest fear - and the first room she went into numbered 214 had a completely different fear. (00:00:56)
Continuity mistake: The Doctor is in a room talking to Amy, Rory and everyone else. He sits at a table where there is a house of cards. The house of cards changes between shots. (00:21:56)
The Wedding of River Song - S6-E14
Continuity mistake: When River sits down by the table as she and Amy are talking and drinking wine, in shots of River, Amy's wineglass is sitting on the corner of the table. In shots of Amy, the glass is first absent, then Amy reaches over, grabs it and takes a sip before resting it on the table with her hand holding the stem, whereas her hand is in her lap in shots of River. (00:40:40)
The Wedding of River Song - S6-E14
Continuity mistake: When the Doctor realises he's picked up a model of the TARDIS in Amy's office, it rotates in his hand between shots, as indicated by the positioning of the sign on the front door. (00:20:55)
The Wedding of River Song - S6-E14
Continuity mistake: During the live chess game, the position of Gantok's hand changes between wide shots and close-ups of the electrified queen piece. (00:06:33)
Continuity mistake: When the Doctor overhears Alfie crying while stirring something in the kitchen, he has the spoon in his hand in the close-up, but his hand is suddenly empty in the wide shot. (00:23:02)
Continuity mistake: During the Doctor's phone conversation with Rita, the handset of her phone keeps switching between ears. (00:32:30)
Continuity mistake: When the Doctor tells Howie that he should continue telling himself the situation is a "CIA thing", he puts his arm around his shoulders twice. (00:11:22)
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)
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)
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)
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.