Under & Out - S3-E11
Plot hole: Gretchen, Lincoln, and Sophia were able to visit Scofield and Whistler in Sona without Gretchen being recognized. She was taken in for questioning in episode 9, but she managed to escape and kill General Zavala and one other guard. The other guards knew that she was the one who killed Zavala but she was still able to sign in for visitation.
Continuity mistake: In the shot where Scofield and Whistler are clinging to the wire from the helicopter, one of the bad guys gets shot and falls out of the helicopter. He falls past the wire, but they're not hanging off it. (00:38:35)
Fire/Water - S3-E2
Continuity mistake: When Scofield has water poured in to his glass the water level isn't even a quarter full, however, when it cuts back the glass is half full. (00:02:00)
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)
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)
Photo Finish - S3-E6
Visible crew/equipment: In the opening scene, a cameraman is visible behind Tracy McGrady. (00:00:47)
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)
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)
Good Fences - S3-E4
Other mistake: In this episode Nieves is killed by Bagwell. At the end of the episode his body is shown being collected by the gravedigger and guards. However, Nieves is still fully clothed. Everytime someone dies in Sona they are stripped of all possessions and clothes by other inmates.
Good Fences - S3-E4
Visible crew/equipment: When Whistler is walking to talk to Sofia for the first time, the camera shadow can be seen to move down the metal fence. (00:11:10)
Interference - S3-E5
Continuity mistake: When the guard leaves he is still holding the rifle scope in his left hand but in the next shot Schofield picks up the rifle scope from the floor.
Orientación - S3-E1
Continuity mistake: Lecharo's girl says "who would have thought it, a famous person in Sona." When she does her top buttons itself up. (00:15:25)
Orientación - S3-E1
Continuity mistake: Sammy kills a prisoner at the start. The position of the dead man changes between camera angles. (00:02:35)
Fire/Water - S3-E2
Continuity mistake: Michael's grip on the paper when he first shows Linc changes between shots. (00:15:20)
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)
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)
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 shooting at the car, Link hits the driver's side window. This bullet hole then moves between shots. (00:32:20)
Answer: Don Self actually worked with Whistler before he died. And Whistler with the bird book actually knew where Scylla was.