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.
Continuity mistake: When Amy's dad stands up to present his speech at her wedding, a tear runs down the right side of Amy's face. In the next shot of her the right side of her face is completely dry.
Continuity mistake: When little Amy looks out the window to see what makes the noise, you can see the TARDIS through her window (it's a little blurry) but when you look through the window properly, it isn't there.
Factual error: When the Doctor, Amy and Rory are on the roof and the Doctor says "The question for now is total event collapse means that every star in the universe never happened", the Gherkin can be seen in the background. However, the Gherkin wasn't built until 2003, whereas this episode takes place in 1996. (00:22:40)
Continuity mistake: When Rory is telling the Doctor that he can afford to take time off because he just saved all of reality, the Doctor leans against the console twice in two successive shots. (00:51:36)
Continuity mistake: When the Doctor is preparing to seal Amy inside the Pandorica, the shoulder restraint goes from raised to lowered between shots. (00:12:42)
Continuity mistake: When the crack in time appearing on the TARDIS' scanner is shown in the "Previously On" segment, the crack is depicted as extending into the leather casing, whereas in the scene in "The Pandorica Opens" where it appeared, it was confined to the screen. (00:00:57)
Visible crew/equipment: When Amy is guesstimating Amelia's age, the camera pans to the right and into a crew member's arm. (00:13:49)
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)
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