Continuity mistake: When Quinn falls in the well, he falls through and subsequently destroys the well cover. At the end of the episode when the Secret Service boys show up, an undamaged cover is lying next to the well, which Kellerman uses to cover it up. (00:29:30 - 00:38:30)
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.
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. (00:38:00)
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. (00:39:35)
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.
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. (00:23:20)
Plot hole: In a previous episode Link says he ditched the gun after he was framed and that he chose the gun the night before. Earlier in the episode, Michael met Link off the street, then went to a bar and met Veronica, then those two go to Michael's apartment. At the apartment, Michael gets the call from Link who is trying to get Michael to talk him out of killing Stedman. But how could he choose a gun the night before when he is asked to kill Stedman and calls Michael on the same day?
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. (00:08:10)
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.