Continuity mistake: When Rory finds his dad on the spaceship, Brian is lying on a gurney next to the two farthest slabs, which are empty. When Amy and the Doctor come through the portal to the spaceship, Brian's gurney is between the two closest slabs, with Rory lying on the closest one, which previously had a completely different person lying on it.
Other mistake: As the Doctor passes a stack of three cubes, the camera is close enough to see the top cube has two small squares intertwined on the side facing diagonally toward the light. He said all were the same, no difference or individuality whatsoever.
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Continuity mistake: When the Doctor is at the Tower of London with Amy and Kate, he claims he needs some air. When Amy follows him she follows him twice, in two different shots. The first time on 'ground view' walking and the second time on 'above view' running.