Continuity mistake: When John and Michael meet with Philly, he has his hands at his sides. Camera changes and they are on the table, clasped. (00:20:40)
Under & Out - S3-E11
Revealing mistake: When Link is dabbing Sofia's burns its clear to see he's not actually making contact with her. Just making the motion. (00:26:10)
Under & Out - S3-E11
Continuity mistake: When T-Bag and Lechero are in the tunnel talking about Michael planning something, Lechero has the crowbar level with his face in some shots and lowered in others. (00:14:00)
And Then There Were 7 - S1-E11
Factual error: D.B. Cooper made his escape on November 24th 1971 with 200k in $20 bills. Westmoreland shows Michael a $100 bill saying it's from the ransom. Impossible. (00:36:00)
Other mistake: When Sara's dad is found dead, Sarah pulled him, so his body dropped on the floor with his key, but this key is different from the other square key that they used it to open his private locker. (00:16:30)
Revealing mistake: When 5 of the escapees are heading to Oswego to get the supplies and Michael tells Lincoln to turn right, you can see it isn't a real car as the steering wheel doesn't turn - Lincoln just moves his hand along the wheel. Watch the grooves and you will see. (00:18:50)
Continuity mistake: Lechero regains command of the prison and dumps the bodies of the two guys off the ledge. His face goes from being clean to full of sand to clean in three short shots. (00:36:20)
And Then There Were 7 - S1-E11
Other mistake: In the first couple of minutes, Michael is sitting on the bed. When he leans forward, you can see his back, but no tattoos. (00:01:00)
Factual error: When Mahone is at MSP International he gets the call about C-Note being in the diner in Benson, MN and says to "fax Fanklin's mugshot to every hospital in southeastern Minnesota." Benson is in West-Central Minnesota, almost 3 hours from Minneapolis, definitely not southeastern MN. (00:03:50)
Other mistake: When T-bag catches Michael in his cell looking for the Allen key, he says, 'What are you doing in my cell?' but he doesn't have his usual southern accent. (00:20:00)
Continuity mistake: When Michael is finishing up the Allen key, he is wearing his grey sweatshirt. Yet when he finishes it and checks it on his tattoo he is wearing his blue shirt over his sweatshirt. (00:36:00)
Factual error: Scofield has two toes cut off. However, his recovery is so quick that it's just plain stupid. He would be limping badly for at least a month.
Riots, Drills and the Devil: Part 1 - S1-E6
Character mistake: Before the riot breaks out in Sick Bay, Dr. Tancredi calls the black inmate "Kwame." The inmate in question is credited simply as "Stroker." "Kwame" is in fact the actor's real first name - Kwame Amoaku. (00:24:15)
Continuity mistake: After the gas canisters are thrown into the rabble, Michael runs back up into his cell and puts his hands on the bunk, they are clean. The shot cuts to T-bag yelling up at him and when the shot goes back to Michael, his hands are covered in blood. (00:32:30)
Suggested correction: When Michael stumbles into his cell and leans against the wall, there are blood trails over his hands. He then stumbles against the bed, and his hands are out of shot but his wrists are still visible. Then, when he falls back against the wall, his hands are visible with the blood trails.
Factual error: They have made it a point that Scofield is incarcerated in a prison in Illinois, and even gets married so he can be eligible for conjugal visits during his stay so he can pass information or items to his "wife" or she to him. In Illinois, conjugal visits aren't allowed. Only something like six states allow them, and this isn't one of them. Totally a plot hole, and since this thing was so carefully planned out, I would think he would run across this information ahead of time.
The Message - S2-E15
Factual error: The 450 Mile road circle discussed by both Michael Scofield and Agent Mahone wouldn't be the size shown as they are traveling by car, not plane or foot. (00:20:15)