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?