Deliberate mistake: When the Doctor visits all his recent companions before he regenerates, he goes to a book signing of A Journal of Impossible Things, written by Joan Redfern's great-granddaughter. When she is signing the book for the Doctor, you can hear the scratching effect from the pen but you can see that the pen isn't touching the paper. (00:59:50)Professor Lazarus
Continuity mistake: When Wilf takes out his revolver and offers it to the Doctor, he's holding it with the grip pointed toward the Doctor. In a wide shot shortly afterwards, Wilf's arm is moving to hold the gun out again, this time with the barrel closer to the Doctor. In the next shot, a close-up of Wilf, the gun is back to its first orientation. (00:25:20)
Continuity mistake: When Shaun and Sylvia run out of the Nobles' house to look as Gallifrey begins to phase in and out next to Earth, Shaun's right hand, which he had on Sylvia's shoulder, changes position between shots just before he runs off looking for Donna. (00:40:40)
Continuity mistake: When Donna, on the phone with Wilf, is surrounded by Master duplicates in the alley behind her house, she has her phone to her ear, but there's a shot where she looks behind her to see two Masters, one of whom is wearing a bowtie, entering the alley, her phone is missing, only to be back by her ear in the next shot. (00:07:05)
Audio problem: During the climax, when the Doctor has Wilf's old service revolver and is alternately pointing it at the Master and Rassilon, there's a cocking sound every time he turns. Not only is the handgun a revolver, so it only needs to be cocked once, the Doctor is only shown actually cocking the gun once, when he first points it at Rassilon. (00:44:10 - 00:45:55)
Other mistake: Shortly after everyone arrives on the Vinvocci ship, when the Vinvocci and the Doctor run through the door on their way to the flight deck, the Doctor comes back to get Wilf, who didn't initially follow because he was mesmerized by the sight of the Earth from orbit. It's obvious that David Tennant went just behind the door and paused briefly before coming back into the room, which is not what the Doctor is supposed to be doing. (00:16:00)
Factual error: The Vinvocci ship is said to be orbiting 100,000 miles above Earth, later refined to 105,000 miles. That's one-third of the distance to the Moon, and the Earth's apparent size from the windows of the ship is far too large for them to be that distance, or even 100,000 kilometres above the Earth's surface. Judging by the Earth's apparent size, the spaceship is actually orbiting 6,000-7,000 kilometres above the planet's surface.