Factual error: When Michael fills the tank with water (below the stock room), he then strips his clothes off, and slides down a pipe and into the water at the bottom of the tank. Since the water level was way above him, the pipe he slid down and the access to get there would have been flooded also. There was no water in the pipe he slid down, so for that area to be dry, it would have to be above the water line.
Revealing mistake: Just after we see the inmate get stabbed there is a shot during the quick montage of one inmate holding the door, while his cellmate climbs up onto the bed for a better look at what is going on. In this very quick shot, the cell door moves despite the fact A wing is on lock down. (00:07:15)
Continuity mistake: This happens in the scene where Lisa is scolding LJ for getting arrested. When LJ says "I don't have a father", he is leaning on the table with his arms crossed. When the shot changes, his arms are uncrossed and in a completely different position. (00:22:25)
Factual error: Lincoln Burrows is scheduled to die on May 11th, 2006. When Veronica learns of the priest's death, we see a wall planner on the wall with May 11th circled in red marker. The day on the wall planner is Wednesday. However, May 11th, 2006 was a Thursday. (00:32:00)
Other mistake: When T-bag catches Michael in his cell looking for the Allen key, he says, 'What are you doing in my cell?' but he doesn't have his usual southern accent. (00:20:00)
Answer: Don Self actually worked with Whistler before he died. And Whistler with the bird book actually knew where Scylla was.