Continuity mistake: We see Link driving with a blue short sleeved shirt on. When he arrives at his destination he's wearing a long sleeved grey undershirt. (00:14:20)
Riots, Drills and the Devil: Part 2 - S1-E7
Continuity mistake: When the Governor arrives his motorcade is on the grass. We then see the warden tell Belleck not to say anything and it cuts back to the motorcade that is just joining the grass. (00:11:20)
English, Fitz or Percy - S1-E5
Continuity mistake: Abruzzi grabs Schofield by the collar when confronting him in the canteen and has a finger raised in one shot but not in the other. (00:11:50)
Rendezvous - S2-E10
Continuity mistake: Near the beginning when the van is chasing the police car, watch the position of the van. It gets nearly alongside the cop car, only to jump behind it when the scene changes. (00:04:40)
Continuity mistake: The blood mark the young inmate leaves on the concrete changes from the time its made until when its found. When its made it is just a small blotch. When Bellick finds it, it is a full on hand print. (00:10:30 - 00:14:25)
Continuity mistake: While Michael is speaking on the phone to the Spanish operator, the small antenna on his phone is raised, but when he starts speaking with Alex and the shot changes back to Michael the small antenna seems to have disappeared. (00:38:15)
Subdivision - S2-E6
Continuity mistake: When the kid returns from the store and opens the trunk, Michael and T-bag both grab a shovel, Michael grabs the green and T-bag grabs the silver handled shovel. The next shot they have switched shovels and keep the switched shovels the rest of the scene. (01:17:30)
First Down - S2-E4
Continuity mistake: When Mahone is looking at the newspaper headlines, the headlines change from being about Abruzzi to Sara between instant camera shots. (00:05:30)
Continuity mistake: At the car dealer where Don Self speaks to the seller, the seller says "How did you find me?" and they are inside the car dealership. Don responds with "I've never lost you". Suddenly when Don answers they are outside the building, like they teleported. (00:13:25)