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
Visible crew/equipment: Just after Amy comes out of the bathroom, a boom mic can be seen popping up behind the agent's shoulder. (00:28:55)
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 Impossible Astronaut - S6-E2
Visible crew/equipment: The astronaut coming out of the lake is twice in series 6: In episode 1, "The Impossible Astronaut", and in episode 13, "The Wedding of River Song." In "The Wedding of River Song", when the helmet of the suit is lifted the astronaut is revealed to be River Song. However, in "The Impossible Astronaut", when the helmet was lifted, a man's beard can be seen. Clearly the use of a double to avoid giving the reveal away too early.
Continuity mistake: When Craig enters the house and falls back when the cybermat is attacking him, his arms are down by his sides, breaking his fall. As he lands, he's suddenly holding the mouse so it can't bite him. (00:25:51)
Continuity mistake: When the Doctor finds Joe's corpse, he walks up to him and puts his hand on his shoulder. In the next shot, facing Joe, the Doctor is suddenly in a completely different position relative to him, behind him as opposed to next to him. (00:15:06)
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)
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: 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)
The Wedding of River Song - S6-E14
Continuity mistake: When the Doctor compares Amy's inaccurate drawing of Rory to the real deal and laughs, in a shot facing Rory the Doctor is shown lowering the picture, than in the next shot facing the Doctor he still has the picture raised. In addition, his grip on the paper changes from holding the bottom of the page to the side, and it also switches hands. (00:23:33)
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 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: When the TARDIS crashes through the ceiling and lands in the tunnel, the side visible to the camera is not the one with the door. The camera cuts away, and when it returns to the TARDIS, on the same angle as before, the door is now facing the camera, as revealed by the sign and St. John's Ambulance medallion. (00:36:16)
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 Impossible Astronaut - S6-E2
Continuity mistake: When the Doctor starts walking over to the lakeshore after the astronaut appears, he's still holding the wine bottle in his right hand. In the next shot where we can see his hand, the bottle is gone, without him having stopped to put it down. (00:06:34)
Continuity mistake: When Alex is hugging George after rescuing him from the peg dolls, George's arms are down in shots facing Alex, but his left arm is up in shots facing him. (00:37:23)
Continuity mistake: When Amy and Rory are searching the darkened kitchen, the flashlight Rory holds switches hands between cuts when it starts turning on and off. (00:13:52)
Continuity mistake: When Idris/the TARDIS stumbles in the junkyard and the Doctor catches her, just before she tells him that one of her kidneys has failed, her right hand, holding a piece of circuitry, moves between in front of his chest in shots facing him and resting on his shoulder in shots facing her. (00:24:48)
Continuity mistake: When the file with the photo of Amy's arm lands in the circle, the thumb in the photo is above the 'T' in 'THIS'. A moment later, the photo's position has turned 180° so that the thumb in the photo is pointed the other way. (00:02:57)
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.