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)
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.
Stupidity: When Michael realises they have too many clowns in the car, they think they can get rid of T-bag. But T-bag says he called someone and told them that "if he doesn't hear from me 5 minutes before the escape or 20 minutes after, he'll call the warden and blow the whistle." They could just go ahead as per usual until T-bag makes the 5 minutes before call, then kill him during the escape, and they still have 20 minutes after the escape.