Other mistake: Between season 1 and 2 the opening there is a shot just as Dominic Purell's name comes up that features a blueprint. On the blue print, there are 2 distances visible - 7' 15" and and 23' 15." There are only 12" in a foot. (00:04:00)
Factual error: There is no prison in the United States that does not strictly segregate Death Row prisoners. They are never, ever allowed contact with the general prison population.
Factual error: When in New Mexico, all the vehicles have license plates on the front. New Mexico only issues one plate, for the rear of the vehicle. Also, at least one of the plates has a Q in the serial. New Mexico only uses Q's on vanity plates.
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.
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".
Audio problem: The episode where Michael and Alex play chicken with their cars, when returning to the road after they scrape cars, there are sound effects of peeling tires. You can't squeal tires on dirt.
Factual error: When Michael fills the tank with water (below the stock room), he then strips his clothes off, and slides down a pipe and into the water at the bottom of the tank. Since the water level was way above him, the pipe he slid down and the access to get there would have been flooded also. There was no water in the pipe he slid down, so for that area to be dry, it would have to be above the water line.
Revealing mistake: Just after we see the inmate get stabbed there is a shot during the quick montage of one inmate holding the door, while his cellmate climbs up onto the bed for a better look at what is going on. In this very quick shot, the cell door moves despite the fact A wing is on lock down. (00:07:15)

Continuity mistake: This happens in the scene where Lisa is scolding LJ for getting arrested. When LJ says "I don't have a father", he is leaning on the table with his arms crossed. When the shot changes, his arms are uncrossed and in a completely different position. (00:22:25)
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)