Continuity mistake: When Bellick is being choked, the guard's arm is constantly changing position around his neck. In some shots, Bellick's neck is in the guard's elbow joint, and in others it's halfway down the guard's forearm. (00:07:45)
Visible crew/equipment: After the bus driver has given Lincoln's description to the police, it cuts to Lincoln driving a car. The camera moves closely in to the car and you can see both the camera and a couple of crew members reflected in the window. (00:13:50)
Continuity mistake: We see Link driving with a blue short sleeved shirt on. When he arrives at his destination he's wearing a long sleeved grey undershirt. (00:14:20)
Revealing mistake: When running to the stash on the beach you can see tracks from previous takes. (00:15:30)
Continuity mistake: At the Buoy, McGrady's hair is constantly changing between shots. (00:21:40)
Visible crew/equipment: S03-E12: When Lincoln gets on the boat, it cuts to a shot from behind him, and the camera's shadow is visible on his back. (00:27:10)
Revealing mistake: When they get on the boat you can see the outline of the wetsuit under Michael's shirt. (00:27:20)
Continuity mistake: When shooting at the car, Link hits the driver's side window. This bullet hole then moves between shots. (00:32:20)
Audio problem: When Whistler steals the truck at the end, he states "Hey my truck" however the audio is a clear overdub. (00:38:15)
Continuity mistake: When Mahone is in the bar at the start, his hand is constantly changing from up at his mouth to down by his side. (00:09:50)
Visible crew/equipment: When McGrady's dad is told to get out of there, a camera shadow is seen to move over the guard's uniform. (00:14:20)
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: The shadows and lighting change throughout the scene with T-bag giving the money to the prisoners. At one point he is in shadow, the next full sun.
Answer: Don Self actually worked with Whistler before he died. And Whistler with the bird book actually knew where Scylla was.