Continuity mistake: During the Doctor and Sarah Jane's conversation in the café while he's repairing K9, when Sarah mentions the events of "The Christmas Invasion" and the Doctor confirms that he was there, the Doctor's hold on a piece of wire from K9's insides changes between shots. (00:17:20)
Continuity mistake: During the Doctor and Sarah Jane's conversation in the café, when Sarah says that she missed him and he responds that she was getting on with her life, in a shot facing Sarah, the Doctor's hands are not visible repairing K9. In the next shot, facing him, his left hand is suddenly on the robot, in a position where it should have been visible in the preceding shot. (00:17:45)
Audio problem: When the Doctor confronts Mr. Finch/Brother Lassar in the school pool, there is a wide shot of the Doctor from across the pool as he asks Finch, "Who are you?" His mouth isn't moving. (00:23:10)
Continuity mistake: When Mickey pulls the blanket off K9 and turns him on to ask if he has anything to get them inside the locked school, K9's right side panel is missing, exposing the wires and circuitry inside him. When he turns up in the cafeteria to help the others escape the Krillitanes, the missing panel has suddenly appeared. (00:34:10)
Continuity mistake: When Mickey enters one of the school's computer rooms, dozens of pupils are busy typing, and every one of them is also wearing headphones. However, once Mickey unplugs the main connection for the computers, and shouts for the students to leave, when the students begin to get up, their headphones have instantly removed themselves from their heads and been placed neatly on the desks next to the computer keyboards. (00:36:25)
Revealing mistake: At the end when Sarah Jane is walking towards the TARDIS and the Doctor opens the doors, the inside of the TARDIS is obviously a painting. (00:39:00)
Continuity mistake: When Sarah Jane is talking to Rose while she's trying to access a computer in the lab, half-sitting on the desk, the right side of Sarah's jacket is bunched up beneath her arm in shots facing her and lying down in shots facing Rose.
Continuity mistake: When Sarah Jane breaks into the school, she has her purse with her. However, after she runs out of the hall with the headmaster's office after hearing some unsettling noises, it disappears, as she no longer has it when she finds the TARDIS hidden in a storage room off the gym.
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.