Continuity mistake: When Brad threatens his ex-cop friend Gary on the phone while leaving a message for him, he says "you better get down your knees and pray to God that I don't find you". Later in the court the recording is "you better get down your knees and pray to God that I never find you".
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)
Under & Out - S3-E11
Revealing mistake: When Link is dabbing Sofia's burns its clear to see he's not actually making contact with her. Just making the motion. (00:26:10)
Under & Out - S3-E11
Continuity mistake: When T-Bag and Lechero are in the tunnel talking about Michael planning something, Lechero has the crowbar level with his face in some shots and lowered in others. (00:14:00)
And Then There Were 7 - S1-E11
Factual error: D.B. Cooper made his escape on November 24th 1971 with 200k in $20 bills. Westmoreland shows Michael a $100 bill saying it's from the ransom. Impossible. (00:36:00)
Other mistake: When Sara's dad is found dead, Sarah pulled him, so his body dropped on the floor with his key, but this key is different from the other square key that they used it to open his private locker. (00:16:30)
Revealing mistake: When 5 of the escapees are heading to Oswego to get the supplies and Michael tells Lincoln to turn right, you can see it isn't a real car as the steering wheel doesn't turn - Lincoln just moves his hand along the wheel. Watch the grooves and you will see. (00:18:50)
Continuity mistake: Lechero regains command of the prison and dumps the bodies of the two guys off the ledge. His face goes from being clean to full of sand to clean in three short shots. (00:36:20)
Deliberate mistake: *SPOILER ALERT* Behind T-Bag is the actor who plays Lechero, and Lechero had just died in the episode. The person was not Lechero, but maybe they didn't have another extra at hand to replace him. 'Time 1' and 'Time 2' are taken from Netflix at the time this was posted. (00:29:46 - 00:30:25)
Continuity mistake: After Sucre and the driver of Stuart's car wreck, another car pulls up behind and starts honking. Cut to a shot from behind the cars and there is a whole line of cars waiting. They weren't there in the opposite angle.
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)
First Down - S2-E4
Continuity mistake: The front licence plate disappears from Link's car as it hits the tree. (00:03:20)
First Down - S2-E4
Revealing mistake: Throughout the entire car chase, you can see through the front window of both cars, including as Linc and Michael are run off the road. However, when the car gets airborne and hits the tree, the glass on the windscreen is now frosted up, so you can see no one is in the car when it hits the tree. (00:03:10)
First Down - S2-E4
Revealing mistake: During the car chase at the beginning, there is a shot of the cars speeding off just before we see the truck approaching. However, look carefully and you will see the truck parked up, waiting to move. (00:02:40)
Answer: Don Self actually worked with Whistler before he died. And Whistler with the bird book actually knew where Scylla was.