Continuity mistake: When the Doctor is shown talking to the Daleks on their spaceship, he is standing several metres away. But the people viewing him from Earth see him standing right in front of them. (00:23:33)
Continuity mistake: When Amy reassures the Doctor that he stopped the bomb, he goes from leaning on a nearby pillar with his arm completely straight to his arm bent. And then his hand changes position a couple more times. (00:34:32)
Continuity mistake: When Churchill says "KBO" before the Doctor and Amy leave, the cigar he was smoking and just lit is suddenly missing. (00:37:09)
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.