Continuity mistake: After the alien abduction, Emmet plans to lead a rescue mission and opens the gate asking "Who's coming with me?" During the sequence, the shadows change completely. At first he is not casting much of a shadow, then it reaches the metal doors, then it stops midway towards it. (00:20:55)
Continuity mistake: In the prologue, the Nazis storm the Bresson residence. The elder Professor Bresson is sitting at his desk, back turned to them. There's an open fountain pen next to him, right by a paper sheet, but when Bresson answers rather defiantly to the bad guys, the paper sheet suddenly has disappeared. (00:02:15)
Continuity mistake: When Hodaka first fires his gun whilst being threatened by the man, the shell casing lands on the ground beside him, right next to his head. A couple seconds later, when Hina goes to help him up so they can run off together, the shell casing has vanished from the ground. (00:22:06)
Continuity mistake: When Santa tells Noelle he's anxious about inheriting his dad's role, the position of his arms is inconsistent between front and side shots.
Continuity mistake: When Bustopher is pulled away from the trash can his face is close to the side with his arms normally stretched. When the angle swaps to a shot from below, his arms are over-stretched and his face is half a meter away from the side. Then it swaps back to the previous angle.