When the Doctor and Rose get into separate elevators to go visit the Face of Boe, the Doctor gets into the left one and Rose into the right. The Doctor gets off at the proper floor from the left elevator. But Rose (being abducted to the lower level by Chip) also gets out of the left elevator, instead of the right one like she should.
When Rose first enters Cassandra's room in the hospital basement, the 20th-century film projector is running. The feed reel is spinning counter-clockwise, and the take-up reel is spinning clockwise; different directions. (This is incorrect, for the way 16 mm films are threaded in this type of projector.)
Then, when the camera's perspective changes to the other side of the projector, both reels are spinning the same direction. (This is correct, as we can see the film now properly threaded through the projector.)
When the Doctor has strapped the bags of IV fluid to himself, the colour of the fluid in the bags strapped to his chest changes between shots.
When Cassandra answers Rose's mobile after being advised by Chip to speak "Old Earth Cockney", she puts the phone to her ear twice in different shots.
In the sequence when Cassandra first takes over Rose's body, the camera cuts to a wide shot of her essence traveling across the dungeon, but the visual effects of the energy restraints and blue psycho-graft beam surrounding Rose are suddenly missing.
It's never explained how the Doctor managed to cure all the test subjects by simply spraying them with the cures, which were shown being used intravenously on the real patients.
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.
The Doctor skips a few New's when he says New (fifteen times) York.