Continuity mistake: When the Doctor and Donna are talking to Caecilius, when they introduce themselves as "Spartacus" and Caecilius makes several guesses as to their relationship, wondering if they're married or siblings, in shots facing them, the Doctor and Donna are standing fairly close together. In shots facing Caecilius, however, the Doctor and Donna are standing much further apart. (00:11:05)
Continuity mistake: After Lucius' arrival, when the Doctor escorts Donna towards the TARDIS, telling her they have to go, which she doesn't agree with, between shots his hands change position between having his right hand on her back, or having both his hands on her shoulders. (00:13:55)
Continuity mistake: When the Doctor and Caecilius are talking while the Doctor examines the hypocaust, Caecilius keeps changing position. (00:17:40)
Continuity mistake: In Lucius' house, when the Doctor pulls the cloth off the shelf with the stone circuits, the position of Quintus' hand on the shaft of the torch he's holding changes between shots. (00:19:10)
Continuity mistake: When Donna changes into contemporary clothing, she has a purple shawl of sorts draped over her dress. In the first shot, she's shown with her hand out from under the cloth, but in the next shot her hand is under the cloth. (00:19:30)
Continuity mistake: When the Sybilline priestesses kneel after the High Priestess speaks, in a shot from the front, Donna, sitting on the altar, has her hands in front of her - she's using her left hand to take the rope off her right wrist. In the next shot, from behind, her hands are at her sides. In addition, the rope still on her right wrist disappears. (00:27:05)
Continuity mistake: When the Doctor explains to Donna how he sees the universe, the distance between them changes several times. (00:31:40)
Continuity mistake: When the Doctor is talking to Evelina at the end, her hair changes position between shots. (00:44:00)
Continuity mistake: When the Doctor and Donna leave as Caecilius, Metella, Evelina and Quintus stand and watch the destruction of Pompeii, the TARDIS changes orientation between shots - in both of them, one from in front of the family and one from behind, the TARDIS' door, with the sign, is visible. (00:45:10)
Continuity mistake: After Metella hands Caecilius the beetle brooch, his hands change position between the close-up and the wide shot. (00:46:10)
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.