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.
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.
Plot hole: In this episode, Kellerman insists that there is no way of identifying Stedman. The brothers ask about DNA, dental records, etc. Kellerman states that they were erased. However, Stedman's DNA can always be tested and compared to that of the presidents. DNA will show that they are siblings. There is no "erasing" that.
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.
Plot hole: They exchange Scylla for the life of the general's daughter. If they counted on him valuing his daughter over Scylla, which he did, they wouldn't have had to steal the cards or break into the vault in the first place. Just kidnap the daughter like they did, tell the general to gather the cardholders and hand over the cards, give them Scylla and let them out.