When Lincoln's dad drives into the junkyard it is very visible that there is nobody in the Mustang with him. After he drives into the enclosure, he gets out of the Mustang, goes over and opens the passenger side door and pulls Lincoln out of the front passenger side seat.
In the scene at the junkyard, when Kellerman is pointing his gun at Lincoln, he alternates between being pretty far away and being really close to Lincoln depending on the angle of the shot.
When Michael sees Sara and the other doctor leave the prison, the two women pass the same setting twice.
When the cop at the crash site talks to Bellick he describes the getaway car as an '06 Mustang'. Then we hear in the background he goes on the police radio and announces they are looking for 'A 2006 Mustang'. However, according to the shows time-line, we are only in May 2005.
When Michael is rejoins the gang after his stay in the psych ward he is telling his team about his progress with the escape plan and how they need to get through that infirmary door, C-Note gives him an idea that they can grab the key like they did for the Pope's office, off a guard. C-Note shouldn't be giving this idea because he wasn't the member of team at that time.