Disconnect - S2-E12
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.
Suggested correction: Not necessarily, The Kansas police would have to do an autopsy to determine cause of death and time of death. T-bag had killed Geary long before Bellick left the voice mail as shortly after, Roy's body arrives at the hospital. So the prosecutor could easily say the voicemail was left after Roy died to try and cover his (Bellick's) tracks.
No the paramedics said he died on the ride over.
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: After the gas canisters are thrown into the rabble, Michael runs back up into his cell and puts his hands on the bunk, they are clean. The shot cuts to T-bag yelling up at him and when the shot goes back to Michael, his hands are covered in blood. (00:32:30)
Suggested correction: When Michael stumbles into his cell and leans against the wall, there are blood trails over his hands. He then stumbles against the bed, and his hands are out of shot but his wrists are still visible. Then, when he falls back against the wall, his hands are visible with the blood trails.
The Message - S2-E15
Factual error: The 450 Mile road circle discussed by both Michael Scofield and Agent Mahone wouldn't be the size shown as they are traveling by car, not plane or foot. (00:20:15)
Call Waiting - S3-E3
Other mistake: Sucre is supposedly passed out, however when Lincoln puts him on the couch his arm moves upward.
Riots, Drills and the Devil: Part 2 - S1-E7
Other mistake: Unlike everyone else in the prison during the riot, Sara Tancredi is not drenched in sweat. In fact, she's not sweating at all.
Subdivision - S2-E6
Continuity mistake: When the kid returns from the store and opens the trunk, Michael and T-bag both grab a shovel, Michael grabs the green and T-bag grabs the silver handled shovel. The next shot they have switched shovels and keep the switched shovels the rest of the scene. (01:17:30)