Continuity mistake: After Lincoln and LJ have been recognized by the waitress, they speed off down a road. During their conversation in the car, whenever we see LJ from (his) right side, his hair is blowing in a strong draft, and is blown away from the temple. In all other shots, his hair is completely calm, and is hanging down and forward, covering his right temple completely.
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.
Plot hole: The Kansas police arrest Bellick for, and he is subsequently convicted of, Geary's murder based in part on a threatening voice mail he left on Geary's phone. But the message's time and date would match the records of Bellick's admittance into the hospital, thus proving him innocent of the crime.
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: When Steadman is watching the agent put the bags that contain the remains of Veronica Donovan into the trunk of the silver car, the license plate changes between shots. The first time we see the car, the plate reads "1029Q", the second time (close-up shot as the agent closes the trunk) it reads "9417X".
Plot hole: Gretchen, Lincoln, and Sophia were able to visit Scofield and Whistler in Sona without Gretchen being recognized. She was taken in for questioning in episode 9, but she managed to escape and kill General Zavala and one other guard. The other guards knew that she was the one who killed Zavala but she was still able to sign in for visitation.
Continuity mistake: Season 2, episode 6. While the guys are digging in the garage, Michael tells Sucre about the website they can use, as C-Note walks in. He closes the door behind him, but misses the catch, and you can see the door start to swing open again behind him as he walks further into the room. Cut to Lincoln for a second, then to a wide shot, and the door is now firmly closed.
Revealing mistake: In the scene where Sarah crashes into the agent's buggy, you see they have been replaced with dummies. When the car first hits, you see one of the dummies fall out, but they are both seated in the next shot. Also you see that it is not Sarah driving but a man.
xx:xx:xxMelissa Jane Swift