Audio problem: Just after the Doctor makes his appearance and Lynda tells him he's "in the house", she appears to continue talking to him but we never hear what she says; instead the scene cuts to the other two housemates complaining about the Doctor's sudden appearance. (00:01:40)
Audio problem: When Rose is sitting in the observation deck, after she looks at the tree cutting and suggests they might be related, when she puts it back down, it makes a "clink" sound, as if made of metal, despite being in a sort of cardboard cup. (00:15:20)
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.