Continuity mistake: In Season 2: Episode 9-"Unearthed" when Bellick is talking to T-Bag in the house, he pulls up a chair to sit down in front of T-Bag. When he pulls the chair out and starts to sit down, the chair is backwards, but in the next shot it's facing T-Bag. (00:38:10)
Continuity mistake: Season 2, Episode 10. When Michael and Sara are driving towards Mahone down Butterfield Road, both cars are seen in one shot and both cars are on a gravel road. In the next clip, seen from Mahone's end of the road, his car is on asphalt.
Continuity mistake: Series 2 - Episode 10. When Sara is to meet Michael at 1681 Butterfield Road Sara looks in the mailbox. She closes the lid, yet the mailbox is seen standing with the lid a bit open. In the next couple of shots the mailbox is completely open, and when they jump in the car and leave, the lid is now closed.
Continuity mistake: In the scene in Panama in the last episode Michael is on the boat and a boy comes along with some sodas. In that scene the sky is overcast. But in the next clip, when the boat is seen further away the sky is clear.
Continuity mistake: Episode 14 - John Doe. Bellick is in the prison, and is being threatened by 'Banks.' As Banks and his crew walk away, in two different shots, you can see an elderly gentlemen (looking like Charles Westmoreland) walk across the screen, left to right. He does this twice, without there being time for him to run around.
Continuity mistake: When Mahone is in Scofield's apartment the show flashes back to an overhead view of Scofield planning on the wall while Mahone is tracing over the holes in the wall from where Scofield was tacking papers up. The mistake is in the flooring, the laminate flooring is a much lighter flooring than when Scofield was there two months prior. (00:21:00)
Continuity mistake: When Steadman takes out his gun, he presses it to the back of Veronica's head. She does not flinch or shy away from the gun, but in the next shot, a close-up of Steadman, the gun muzzle is pointed at the camera with Veronica off-screen, and so the gun is suddenly not touching her. (00:22:40)
Continuity mistake: When Steadman is watching the agent put the bags that contain the remains of Veronica Donovan into the trunk of the silver car, the license plate changes between shots. The first time we see the car, the plate reads "1029Q", the second time (close-up shot as the agent closes the trunk) it reads "9417X". (00:37:20)
Continuity mistake: When Lincoln and Michael are talking on the little pier, Michael talks about Westmoreland and his relationship to the truth. Lincoln has his head turned towards Michael through this, but as Michael says "There'd be no reason for him to lie about it", the angle changes and Lincoln is suddenly staring straight ahead, with no time to turn his head between shots.
Continuity mistake: When Michael is sitting in the park he's staring at the front page of the newspaper. As the camera follows a man in the park you can see that Michael has opened to the midpages, but in the next shot Michael is looking at the front page again, before opening it another time. (00:02:00 - 00:02:30)