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)
Revealing mistake: When the girl raises her visor to reveal herself in the spacesuit, the cracks in the visor from where it was shot earlier are drawn on. (00:20:22)
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)
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.