Continuity mistake: When the Doctor is listing questions about what exactly the ghosts are, he goes from gesturing with his left hand in the close-up to gesturing with his right in the wide shot. (00:17:17)
Audio problem: Shortly after arriving at the Drum and taking shelter in the Faraday cage, when the Doctor is looking out the window in the door at the ghosts, he says "What are you?" His jaw doesn't move.
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.