And Then There Were 7 - S1-E11
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. (00:09:40)
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?
Plot hole: C-Note says about pulling a simple bump and grab on The Key like they did before. However, when Abruzzi and his men get The Key the 1st time, C-Note wasn't in the group then. It is extremely unlikely they would divulge this trivial piece of information as the issue is long since resolved. (00:03:50)
Rendezvous - S2-E10
Plot hole: Linc is arrested in Wilcox, Arizona and is rescued by his father's people. They then take him to Trinidad in Colorado, an 8 and a half hour journey by car - they are seen in the same van. However in those 8 hours, it's not noticed that a) The police unit had been attacked and b) Lincoln Burrows, one of the 8 most wanted men in the USA, had escaped. Surely in 8 hours someone would have noticed. (00:07:35)
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.
Under & Out - S3-E11
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.