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)
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.
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)
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)
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.
Character mistake: Mahone is very smart and meticulous, similar to Schofield. He has a good knowledge of forensics as shown throughout the show. However he shoots Tweener, and places the gun in his hands after shooting him. He would know that the blood on Tweeners hands would show he wasn't holding the gun when he was killed due to blood spatter behind behind the weapon. (00:40:20)
Continuity mistake: When Brad threatens his ex-cop friend Gary on the phone while leaving a message for him, he says "you better get down your knees and pray to God that I don't find you". Later in the court the recording is "you better get down your knees and pray to God that I never find you".
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)