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 Craig enters the house and falls back when the cybermat is attacking him, his arms are down by his sides, breaking his fall. As he lands, he's suddenly holding the mouse so it can't bite him. (00:25:51)
Continuity mistake: When Amy and Rory are searching the darkened kitchen, the flashlight Rory holds switches hands between cuts when it starts turning on and off. (00:13:52)
Continuity mistake: When the Doctor finds Joe's corpse, he walks up to him and puts his hand on his shoulder. In the next shot, facing Joe, the Doctor is suddenly in a completely different position relative to him, behind him as opposed to next to him. (00:15:06)
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.