Visible crew/equipment: As Sally enters the living room in the abandoned house, in the shot where she walks through the doorway, a cameraman holding the camera can be seen reflected in the window of the door next to her. (00:00:35)
Continuity mistake: The cab Donna's in passes a red vehicle on the bridge. A second later, it's nowhere to be seen looking back. (00:12:15)
The Family of Blood (2) - S3-E9
Revealing mistake: The pyrotechnic mortars used in the destruction of the Family's ship are visible in the shots leading up to their detonation. As the Family run from their ship through the field, the mortars are visible against the branches behind them. Shortly afterwards, they detonate, creating the illusion that the invisible craft has exploded.
Audio problem: Near the beginning of the episode when we first see Bannakaffalata, he says "Christmas is funny", yet his lips don't match what he is saying. (00:01:45)
The Family of Blood (2) - S3-E9
Continuity mistake: When Timothy opens the watch into the girl's eyes, Jeremy Baines shouts "Time Lord", then a few seconds later; "What are we waiting for. Attack!" There is then a shot looking down on the scarecrows, Jeremy and Jenny. If you look closely at Jeremy Baines, it's a different actor playing him. (00:16:20)
Evolution of the Daleks (2) - S3-E5
Other mistake: After the hybrid Dalek Sec explains the Daleks' plan to harness the power of a solar flare to the Doctor, when the Doctor asks how many minutes until the flare arrives, Sec says it's in 11 minutes. A fair amount of action and backstabbing later, when the Doctor and Laszlo arrive at the top floor of the Empire State Building and after the Daleks take back control of the elevator, the Doctor says that the solar flare arrives in 6 minutes. It is a considerable stretch for everything that happens between those two moments to take place in only five minutes.
Revealing mistake: When Lilith bespells Shakespeare to write the end of Love's Labour's Won the way the Carrionites want it, there are several shots where a white fleck of some kind is visible in the lower centre of the screen, stuck to the camera lens. (00:17:10)
Last of the Time Lords (3) - S3-E13
Factual error: When time is seen rewinding after the destruction of the Paradox Machine, the Earth and Moon are seen rotating and orbiting backwards. The Moon is depicted far closer to Earth than it actually is. (00:37:40)
Factual error: When the Royal Hope Hospital is transported to the Moon, the area it is in is dark, indicating they are on the side of the Moon not currently facing the Sun. However, in a wide shot of the hospital on the Moon, something that looks like the Sun is visible, something that the illumination of the landscape and the Earth shows cannot be visible. (00:07:40)
Utopia (1) - S3-E11
Other mistake: The stet radiation in the red room is able to disintegrate living beings, with the exception of the immortal Jack. People not going in the room are shown to stay out of the line of the door when it's being opened, lest they be disintegrated. When Jack comes out of the room after having finished in there, the Doctor, telephoning the rocket, is in line with the open door yet remains completely fine. (00:35:15)
Utopia (1) - S3-E11
Other mistake: When Professor Yana shows Martha his pocket watch, which she comes to realise is a Chameleon Arch, she initially finds it familiar from the appearance of the back, and eventually asks him if she can see the front. Before she eventually sees the front of the watch, there is a shot where the front is hidden to the camera, but should be perfectly visible to Martha, just as Yana says "It's old. It's not meant to be." (00:34:40)
Character mistake: The question to unlock one of the doors asks for the next number in the sequence 313, 331, 367. The Doctor gives the answer as 379 with a convoluted (albeit correct) explanation of happy primes, but there are much simpler solutions. The difference between the first and second numbers is 18 and the difference between the second and third is 36 (which is 2 x 18), suggesting that the difference between the third number and the next could be either 54 (= 3 x 18), giving 421 as the next number, or 72 (= 2 x 36), giving 439. It's likely that the Doctor would see that the answer is ambiguous, and yet he confidently states that the most complicated answer is correct. (00:08:45 - 00:09:15)
Suggested correction: If you know what a happy prime is, like the Doctor does, it might be simpler than your idea because you gave 2 options - 421 and 439. The idea of a pattern is there should be only one answer that fits, which would be the case if they're all happy primes.
Character mistake: After the Carrionites kill Lynley, the Master of the Revels, by using the doll to make him drown on dry land, the Doctor says, while examining the body, that he's never seen a death like it. In the Third Doctor serial "The Mind of Evil", involving a monster that could make people relive their worst fears, a character died in exactly that fashion. (00:13:10)