The Unicorn and the Wasp - S4-E7
Factual error: In real life, Agatha Christie's famous disappearance occurred in December 1926. This episode is quite plainly not set in winter, what with the outdoor garden party and lush green foliage.
The End of Time: Part Two - S4-E18
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.
Plot hole: After getting out of the Pyrovile escape pod, the Doctor and Donna start running back to Pompeii. In the process, they are somehow able to outrun what appears to be a pyroclastic flow. Pyroclastic flows can reach speeds of up to 700 kph, and should be impossible for them to outrun. (00:38:15)
Continuity mistake: After the Doctor and Wilf get off the seniors' bus, they're waving goodbye. In a close-up shot, the Doctor is waving with his right hand, but in a wider shot immediately afterwards, he's switched to his left hand. (00:25:10)
Continuity mistake: At the end, when the Doctor is watching his hand starting to glow, shots from his point of view show that he's holding it vertically. But shots from the opposite view show that he's holding it horizontally. (00:43:39)
Chosen answer: The Master knows that deep down, he deserves death for the crimes that he's committed throughout his life, and since he regards The Doctor as his arch-foe, he expects it to be at his hands. The fact that The Doctor is still willing to forgive him for all of his crimes hurts him more deeply than death would.
Captain Defenestrator