Continuity mistake: When Cassandra, possessing Rose, confronts the Doctor after he wakes up in one of the clone pods and tells him how she intends to kill him, her hand changes position between the shot from inside the pod, when she rests her hand on the front, and the next shot from outside the pod. (00:24:20)
Continuity mistake: When Rose gets into one of the hospital's elevators early in the episode, stock footage of an elevator descending is shown. When the Doctor, Rose and Cassandra (possessing her) go into an elevator shaft later on, it looks and is shaped completely differently. (00:34:05)
Continuity mistake: When the Doctor is attaching the ring device to the elevator cable, the position of his hand as he's holding it in place changes. (00:34:10)
Plot hole: Those people created for medical experiments cannot run. In fact they can barely walk, so how come they can climb nearly as fast as Rose? What's more, when you see them climbing, they seem to have little ability to coordinate hand over hand. Even with the delay brought on by the cat-woman-thing, they should not have been able to keep up with her.
Continuity mistake: When Chip/Cassandra finishes the line about being a walking doodle, he's smiling. After the cut, he's straight faced.
Character mistake: When the Doctor and Rose are walking back to the TARDIS at the end, he explains to her that Queen Victoria was hemophiliac. She wasn't. She was a carrier of the disease due to a mutation in one of her parents' reproductive cells (probably her father, Edward, Duke of Kent, because he was in his fifties when Victoria was born), but since she only had it in one of her X chromosomes, she didn't actually suffer from it as the gene for it is recessive, which is why most hemophiliacs are male. It is true that several of her children inherited the gene, and one of her sons was hemophiliac, but not Victoria herself. (00:40:55)
Factual error: The Koh-i-Noor, as depicted in this episode, looks absolutely nothing like the real diamond. The episode's gemstone is about the size of the palm of the Doctor's hand, and shaped in a stereotypical brilliant cut. The real Koh-i-Noor is much smaller and oval-shaped.
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.