Other mistake: Near the start of the season Lincoln gets a bullet wound to his leg, However there is no exit wound, revealing the bullet is lodged in his leg. Yet he is able to run and move around with relative ease just hours after being shot.
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)
Odd Man Out - S1-E12
Visible crew/equipment: When C-note's associates get back in their truck a stage light and equipment is reflected in the paintwork. (00:38:00)
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)