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 Cassandra reveals her presence to the Doctor, she starts off by turning him to face her, then pulling his tie out of his jacket with her right hand and tightening the knot with her left hand, in a shot facing him. In the next shot, facing her, she has her right hand holding the knot of the tie. Finally, just before Cassandra reveals her identity to the Doctor, shortly later, which hand is holding the tie changes again. (00:23:20)
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)
Doctor: So, that's the trap. Or the test or the final judgment, I don't know. But if I kill you, I kill her. Except that implies, in this big grand scheme of Gods and Devils, that she's just a victim. But I've seen a lot of this universe. I've seen fake gods and bad gods and demi-gods and would-be gods - out of all that - out of that whole pantheon - if I believe in one thing... Just one thing... I believe in her.