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.
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)