Revealing mistake: In the opening scene the Doctor and Donna are speaking over the phone. The purple phone Donna is holding shows the slot where a cable should be plugged in, but there is none. (00:00:25)
Suggested correction: This shouldn't be considered a mistake. While it's true in real life this phone has a slot for a cable, they're on an alien planet and this is unknown technology. In-universe there's no way of knowing what that slot is for, and there's no reason to think the phone needs to be plugged into anything.
Revealing mistake: When the Doctor and Donna run back inside the TARDIS to find the console room lit up in red and the Cloister Bell ringing, what's visible outside of the doors as they run in isn't the bright Shan Shen street the TARDIS is parked on but the dark soundstage the set was built in. (00:47:49)
Revealing mistake: When Torchwood is transmitting a signal to the Doctor, there is an overhead shot of Cardiff in which several shoppers are idly walking through apparently deserted streets. (00:31:55)
Revealing mistake: The Cyber-Leader has a clear section in the top of its head through which its brain can be seen. The brain in question is very obviously plastic.
Revealing mistake: Adams, the female Vinvocci, has a tendency to wrinkle her forehead, which makes the fact that her spiky head is a cap the actress is wearing very obvious.
The End of Time: Part Two - S4-E18
Revealing mistake: When Addams is telling Rossiter not to respond the Master's message, a patch of non-green skin can be seen on her face showing where the makeup wasn't fully painted on. (00:27:50)
The End of Time: Part Two - S4-E18
Revealing mistake: When the Doctor is being rolled down the stairs whilst he is strapped to the chair, it is apparent that in the wide shots, it is a dummy in the chair and not the Doctor. In the wide shots, the Doctor is sitting virtually still and motionless, but in the closer shots, he is fidgiting.
Revealing mistake: When an Atraxi ship appears over the village green, there's a shot where the Doctor, Amy and Rory turn to look at it, and they're standing in bright sunshine with their shadows visible - despite the fact that the Atraxi have surrounded the planet with a forcefield that dims sunlight, so those shadows shouldn't be possible. (00:36:05)
Revealing mistake: When the TARDIS dematerialises and causes wind to blow against Churchill and Amy, their clothes are affected - but the cigar smoke in the air is unaffected, and actually drifts towards the vanishing TARDIS. (00:14:25)
Revealing mistake: When the Doctor's jacket is being held by a Weeping Angel while he's monologuing about why they haven't killed him yet, he moves at one point and the Angel's hand moves with him, despite the fact that they're normally effectively stone in situations like this. (00:12:16)
The Vampires of Venice - S5-E6
Revealing mistake: When the Doctor begins climbing a pillar on top of the bell tower, we can see white sky on the central arch. Two other arches in the very same shot show really dark CG sky. (00:42:17)
Revealing mistake: When the Cyberman arm is shooting at the Doctor and Amy, just after the Doctor jumps out to draw its fire, Amy leans on the Pandorica and you can see it bend in, revealing that it's made out of plastic or something. (00:20:42)
Revealing mistake: As Amy stands where she is told, a cable comes towards her feet. As it does, a black thread can be seen pulling it up to wrap around her leg. (00:21:39)
Revealing mistake: In the museum after the Doctor, Amy, young Amy and Rory escape the Stone Dalek, the Doctor uses the Vortex Manipulator to go back in time to tell Rory in 102 AD to let him out of the Pandorica. The third time he goes back, Amy moves despite being dead. (00:19:38)
Revealing mistake: When the Doctor travels back in time after being shot by the stone Dalek, falls down the stairs and tells himself that he has 12 minutes to live we never see either of the 2 Doctors' faces onscreen at the same time, and if you look at the hair on the Doctor that's dying it is completely different to Matt Smith's. That's because it is Gordon Seed, Matt Smith's stunt double.
The Impossible Astronaut - S6-E2
Revealing mistake: When the Doctor is struck by the green light emitted from the astronaut, his right thigh momentarily disappears due to the animation. (This is even more visible when looking at the still of this shot on the Doctor Who website). (00:07:06)
Revealing mistake: When the girl raises her visor to reveal herself in the spacesuit, the cracks in the visor from where it was shot earlier are drawn on. (00:20:22)
A Good Man Goes to War - S6-E8
Revealing mistake: Several of the hallways in Demon's Run, particularly the one where Madame Kovarian has the baby brought to her and the one the Doctor's standing in when he realises where Amy and Rory's baby was conceived, are the repainted sets of the TARDIS hallways from "The Doctor's Wife", three episodes before.
Revealing mistake: When River grabs a gun off one of the soldiers she just knocked out with regeneration energy, the actor sits up slightly, even though the soldier is supposed to be unconscious. (00:24:44)
Revealing mistake: Mels is shot in the stomach by Hitler, leading to her regeneration. Rory, when checking the wound, says he's going to try and stop the bleeding. However, when she stands up while glowing with regeneration energy, and in every scene afterwards where Mels/River is wearing that dress, there is no bullet hole or bloodstain visible.