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 Impossible Astronaut - S6-E2
Continuity mistake: When the school bus pulls up to drop Amy and Rory off in Monument Valley, there are no other vehicles in the area. When the bus pulls away, the Doctor has suddenly appeared with a vintage station wagon, parked by the side of the road where it should have been perfectly visible. And he was sitting on the hood, implying he'd been waiting there for a bit. (00:02:45)
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)
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)
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)
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)
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)
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)
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)
Continuity mistake: After River shoots the last of the Silence, she turns her gun flat side out, and muzzle up. After the angle change, she does it again. (00:37:58)
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)
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: 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 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: The pirate that Toby cuts on the hand with a sword in order to make him stay in the magazine is gone when the Doctor and Captain Avery return, but reappears on the spaceship at the end with the rest of the crew.
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)
Continuity mistake: As the Doctor talks to Idris/TARDIS, he reaches into his coat. When the angle changes, he reaches in again. (00:18:20)
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/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/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)
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.