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: 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: The Doctor's hair changes from the time he realises Rory is there to when the Pandorica is unlocking.
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: 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 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 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)
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.