Vincent and the Doctor - S5-E10
Factual error: By the time the Doctor and Amy meet him, Vincent van Gogh had already mutilated his ear. He should be missing part of his left earlobe.
Vincent and the Doctor - S5-E10
Continuity mistake: Amy's tights appear to be gone when she's watching Vincent paint the church. Previously whilst walking to the church they are on.
The Lodger - S5-E11
Continuity mistake: When the Doctor is flipping through a book while talking with Amy on his earpiece, in the close-up shot he's using his right hand, but in the wide shot is using his left hand, going through the pages the other way. (00:12:10)
Continuity mistake: At the beginning, when the Doctor takes Amy to planet One, he holds out his hand for Amy to take hold of when they're about to leave the TARDIS. When you see her from the back, Amy lifts her hand wearing her red fingerless gloves. But when it switches shot and faces Amy from the front, she takes the Doctor's hand wearing no gloves. When she steps out of the TARDIS, her gloves are on again. (00:04:54)
Continuity mistake: When the Doctor, River and Amy are exploring, several shots of him are obviously reversed because of the flipped hair part and the fact that he's using the sonic screwdriver in his left hand in them. (00:09:00)
Continuity mistake: When the Doctor and River open the door to the room with the Pandorica and walk inside, River's right arm, with which she's holding a torch, changes position between shots, as does how she's holding the torch. (00:11:04)
Other mistake: As Amy, River and The Doctor enter "the Underhenge" River says "More than just a fairytale." This is a reference to The Doctor saying pretty much the same thing to River at the end of S5 E5 when she says she will see him again "when The Pandorica Opens." This moment has not happened for River yet, it is still in her future. So how can she "call back" to it? (00:11:48)
Continuity mistake: When River is talking to the Roman commander after disintegrating a piece of furniture with her pistol, she is shown raising her fingers from the pistol's grip in a shot facing the commander. However, in all following shots facing her, her fingers are still lowered. (00:17:50)
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)
Continuity mistake: The Doctor's hairstyle alternates from parted over the left side to a right side part and back while standing by the Pandorica. (00:27:40)
Continuity mistake: When River is looking at Amy's book about Pandora's Box, her grip on it changes between shots. (00:35:56)
Visible crew/equipment: When the Cyber-arm is shooting at the Doctor and Amy, there is a brief shot when the Doctor is talking where you can see the crew member who is shooting at them.
Continuity mistake: The Doctor's hair changes from the time he realises Rory is there to when the Pandorica is unlocking.
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)
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)
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)
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)
Chosen answer: 1) When Stephen Moffat took over he ignored a lot of what had been developed before (there is not in-universe answer). 2) It would have killed Rose, so the Doctor absorbed the energy. His body regenerated before the energy could do a significant amount of damage that would prevent regeneration.