Continuity mistake: When the Doctor takes the piece of TARDIS shrapnel out and looks at it, he's holding it differently between the close-up and the wide shot. (00:44:05)
Vincent and the Doctor - S5-E10
Continuity mistake: When Vincent asks Amy "One of my favourite 'whats'?" his right arm is suddenly lowered even though he was just holding up one of his paintings. (00:06:40)
Vincent and the Doctor - S5-E10
Continuity mistake: Amy's tights appear to be gone when she's watching Vincent paint the church. Previously whilst walking to the church they are on.
The Lodger - S5-E11
Continuity mistake: When the Doctor is flipping through a book while talking with Amy on his earpiece, in the close-up shot he's using his right hand, but in the wide shot is using his left hand, going through the pages the other way. (00:12:10)
Continuity mistake: At the beginning, when the Doctor takes Amy to planet One, he holds out his hand for Amy to take hold of when they're about to leave the TARDIS. When you see her from the back, Amy lifts her hand wearing her red fingerless gloves. But when it switches shot and faces Amy from the front, she takes the Doctor's hand wearing no gloves. When she steps out of the TARDIS, her gloves are on again. (00:04:54)
Continuity mistake: When the Doctor, River and Amy are exploring, several shots of him are obviously reversed because of the flipped hair part and the fact that he's using the sonic screwdriver in his left hand in them. (00:09:00)
Continuity mistake: When the Doctor and River open the door to the room with the Pandorica and walk inside, River's right arm, with which she's holding a torch, changes position between shots, as does how she's holding the torch. (00:11:04)
Continuity mistake: When River is talking to the Roman commander after disintegrating a piece of furniture with her pistol, she is shown raising her fingers from the pistol's grip in a shot facing the commander. However, in all following shots facing her, her fingers are still lowered. (00:17:50)
Continuity mistake: The Doctor's hairstyle alternates from parted over the left side to a right side part and back while standing by the Pandorica. (00:27:40)
Continuity mistake: When River is looking at Amy's book about Pandora's Box, her grip on it changes between shots. (00:35:56)
Continuity mistake: The Doctor's hair changes from the time he realises Rory is there to when the Pandorica is unlocking.
Continuity mistake: When the crack in time appearing on the TARDIS' scanner is shown in the "Previously On" segment, the crack is depicted as extending into the leather casing, whereas in the scene in "The Pandorica Opens" where it appeared, it was confined to the screen. (00:00:57)
Continuity mistake: When the Doctor is preparing to seal Amy inside the Pandorica, the shoulder restraint goes from raised to lowered between shots. (00:12:42)
Continuity mistake: When Rory is telling the Doctor that he can afford to take time off because he just saved all of reality, the Doctor leans against the console twice in two successive shots. (00:51:36)
Continuity mistake: When Amy's dad stands up to present his speech at her wedding, a tear runs down the right side of Amy's face. In the next shot of her the right side of her face is completely dry.
Continuity mistake: When little Amy looks out the window to see what makes the noise, you can see the TARDIS through her window (it's a little blurry) but when you look through the window properly, it isn't there.
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)
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.