Continuity mistake: Alexander Mahone reveals his so called past to Tweener and shows pulls out 2 pills from his pen, however next time we see the pills there are 3. (00:12:10 - 00:13:20)
Continuity mistake: The Key that falls out of the governor's pocket when Sara is trying to save him is not the same as the one she picks up. (00:24:00 - 00:25:00)
Continuity mistake: Tweener is talking to his lover then has his arms up on his head, then the FBI catch him and tell him to put his hands up. (00:34:36)
Continuity mistake: When Tweener goes to the house from the girl from Utah he has his hands on his head, then not. (00:34:40)
Continuity mistake: You can see David with his hands behind his head, but in the next shot he still has his hands beside him, and only later places them behind his head. (00:34:48)