Continuity mistake: When Amy lies down on the tree stump, her hair is all over her face, but on the wide shot her hair is behind her head. (00:12:46)
Continuity mistake: After the Doctor finds out River's in Stormcage, when he pulls out of the pocket computer to look at the readings from the time crack, it rotates in his hand between shots. (00:19:24)
Continuity mistake: In the last scene, when Amy attempts to seduce the Doctor, she pulls his suspenders off his shoulders and he pulls them back on. As a result, the suspenders change position between shots.
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.