Revealing mistake: Near the end, when Michael is unscrewing the sink before kicking the wall in, watch his hands in the foreground while he is talking to Sucre. Just when Sucre says "But what you were doing up there in the infirmary." Michael starts using his fingers to take the bolt out. You can see that there is no bolt, just him turning air, with a mystery 'unscrewing' sound effect.
Continuity mistake: In the scene where LJ comes to visit Lincoln and admits to breaking the coffee table, LJ's hand moves between shots. When Lincoln is shown, you can see LJ sitting in front of him with his chin resting on his hand. When the shot changes to close-ups of LJ, his hand is down and completely out of the shot.
Continuity mistake: Before being sent to psyche ward, Michael had brutally hurt his right hand by repeatedly punching it at the cement wall of the cell. But moments later,seen in psyche ward after being cleaned up, there's no sign of any hurt on that hand, even no gauze covering at all. We can see his normal good hand.
Revealing mistake: After Pope enters Scofield's cell to see the escape hole, we see him standing outside the cell looking out at everyone throwing toilet tissue etc. If you watch closely right after we see a guy pulling his pillows toward him to tear up, it cuts to another inmate who is throwing stuff out as well. Only thing is, we see the cell door slides to the side slightly which would indicate that the cell doors where not locked. In the event of an escape, lockdown would happen immediately, with all cell doors locked with the prisoners inside their cells.
Continuity mistake: In Episode 14, "The Rat", when Lincoln and Dr. Tancredi are in his cell together, he says "How it gonna feel when they tighten the belts". He then turns his head so that he is looking the doctor in the eyes, but when the angle changes, he is staring directly in front of himself, and his head is not turned at all.
Continuity mistake: When Michael is supposed to be in Pope's office holding the support for the Taj Mahal so it didn't come unglued, Abruzzi placed the makeshift key in the lock of the door, allowing Michael to escape to get back with the other inmates. When Michael opens the door and it's unlocked, the key is in the deadbolt. As he shuts the door behind him, the key is in the lock of the door knob.
Other mistake: When Michael climbs up the rope to get to the room below the infirmary, the rope is hanging from the manhole cover, but he still manages to lift the cover whilst hanging from it. In the next shot where he looks down the manhole, its clear that there is nothing other than the rope he could have held on to while lifting the cover. An impressive accomplishment, defying the laws of gravity.
Factual error: Veronica pulls Lincoln's file after being informed that The Bishop was killed in his home. The file lists Lincoln Burrows as the Plaintiff, and State of Illinois as the defendant. Given that it was a murder trial, these should be reversed.
Plot hole: When Scofield comes back after visiting his wife, Fernando announces his arrival. However the problem is, everyone is inside digging the hole. As Fernando walks in along with Scofield, it leaves no one outside watching for guards. The guys are at least smart enough to keep the watch outside instead of all staying inside. If a guard shows up unnoticed, they are screwed.