First Down - S2-E4
Continuity mistake: Link pulls the clip out of his pocket, and the way he holds it changes between shots. (00:39:00)
Continuity mistake: On the tombstone in the previous episode, Michael's date of death is 11.4.2005. But in this episode, when Linc goes to the graveyard to visit Michael's grave, his date of death is 11.4.2010. It is also a different grave from the original, as the original was in South America beside the beach, and here we are led to believe it is in New York. (00:50:50)
Factual error: When Michael fills the tank with water (below the stock room), he then strips his clothes off, and slides down a pipe and into the water at the bottom of the tank. Since the water level was way above him, the pipe he slid down and the access to get there would have been flooded also. There was no water in the pipe he slid down, so for that area to be dry, it would have to be above the water line.
Other mistake: When Michael climbs up the rope to get to the room below the infirmary, the rope is hanging from the manhole cover, but he still manages to lift the cover whilst hanging from it. In the next shot where he looks down the manhole, it's clear that there is nothing other than the rope he could have held on to while lifting the cover. An impressive accomplishment, defying the laws of gravity. (00:38:00)
Other mistake: If the show takes place in May, when Lincoln is scheduled to be executed, why is it snowing?
Suggested correction: It does occasionally snow in such months. There is no rule about weather being certain. It's just what we consider usual for each season, e.g. winter = cold. Characters even comment on very "variable" weather in state.
Other mistake: Michael goes to Fox River in April. Maricruz gets pregnant in the same month. In mid-June, when Michael get arrested in Panama, she's still pregnant. That's 2 months. He was in there for about 2 weeks, due to his deal with the company. Therefore, he would have escaped Sona at the end of June or the start of July. The start of Season 4 is set 3 weeks after the escape from Sona, so Maricruz should be 3 months pregnant, but gives birth at the start of season 4, meaning that the baby is 6 months early but looks very healthy.
Other mistake: The psychologist shows Michael a photo of his family with his Mom, Dad, Michael and Lincoln but Michael never actually met his father when he was young.
Revealing mistake: In the final scene you can see Abruzzi in his cell where they have reused shots from series 1 in Fox River.
And Then There Were 7 - S1-E11
Continuity mistake: When chasing LJ through the woods, Quinn's wounds go from his right side to his left side and back. (00:29:10)
Audio problem: Bellick gets shot in the leg and screams but in the brief shot we see his face during the sound, he isn't screaming at all. (00:23:20)
Photo Finish - S3-E6
Visible crew/equipment: In the opening scene, a cameraman is visible behind Tracy McGrady. (00:00:47)
And Then There Were 7 - S1-E11
Continuity mistake: LJ is dragged into a second room and is facing away from the door. Camera changes and now he is facing the door. (00:13:40)
Plot hole: In a previous episode Link says he ditched the gun after he was framed and that he chose the gun the night before. Earlier in the episode, Michael met Link off the street, then went to a bar and met Veronica, then those two go to Michael's apartment. At the apartment, Michael gets the call from Link who is trying to get Michael to talk him out of killing Stedman. But how could he choose a gun the night before when he is asked to kill Stedman and calls Michael on the same day?
Factual error: Lincoln Burrows is scheduled to die on May 11th, 2006. When Veronica learns of the priest's death, we see a wall planner on the wall with May 11th circled in red marker. The day on the wall planner is Wednesday. However, May 11th, 2006 was a Thursday. (00:32:00)
Plot hole: C-Note says about pulling a simple bump and grab on The Key like they did before. However, when Abruzzi and his men get The Key the 1st time, C-Note wasn't in the group then. It is extremely unlikely they would divulge this trivial piece of information as the issue is long since resolved. (00:03:50)
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: In season 1 Lincoln says his mother died of liver cancer. In season 4 they said she died from a brain tumour.