Continuity mistake: When John and Michael meet with Philly, he has his hands at his sides. Camera changes and they are on the table, clasped. (00:20:40)
Factual error: They have made it a point that Scofield is incarcerated in a prison in Illinois, and even gets married so he can be eligible for conjugal visits during his stay so he can pass information or items to his "wife" or she to him. In Illinois, conjugal visits aren't allowed. Only something like six states allow them, and this isn't one of them. Totally a plot hole, and since this thing was so carefully planned out, I would think he would run across this information ahead of time.
Continuity mistake: When Patterson brings the tray to Linc at the start, the position of the milk on the tray changes between shots. Note the corner of the tray. (00:09:40)
Continuity mistake: C-Note puts some of the rubble on the table when talking to Michael. The rubble changes when Michael brushes it off the table. A particularly large rock appears that wasn't there before. (00:37:50)
Continuity mistake: When Link slides his last meal request under the door, the card turns and one corner is facing the door. Camera cuts and now the card has turned and one edge is parallel to the door. (00:29:20)
Continuity mistake: Sarah states she is 29 and is holding a piece of paper up on the notepad. Camera cuts and she lifts the bit of paper again. (00:14:25)
Answer: Don Self actually worked with Whistler before he died. And Whistler with the bird book actually knew where Scylla was.