Continuity mistake: The Key that falls out of the governor's pocket when Sara is trying to save him is not the same as the one she picks up. (00:24:00 - 00:25:00)
Audio problem: On the boat, Chaco comes up to DeJesus and asks what's up. When DeJesus answers in Spanish, what he says and his lips are unsynchronized. (00:15:00)
Continuity mistake: When Tweener goes to the house from the girl from Utah he has his hands on his head, then not. (00:34:40)
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.
Continuity mistake: At the end in Sona, Michael is walking down a corridor. He gets over halfway and spots a lad in a red top having taken drugs. After this we see Michael again and he's back at the start of the corridor. Note the door on screen left and the number of light fittings. (00:40:30)
Continuity mistake: When trying to write the letter for Kirsty, Paul puts his hand down by the side of the paper. However it's suddenly on the paper in the next shot. (00:18:30)
Continuity mistake: When Linc attacks Agent Mahone, he says "toss me the handcuffs." Later we see a flashback to that scene and Linc says "Give me the handcuffs" (00:16:20 - 00:39:00)
Continuity mistake: When President Reynolds steps out of her limo, one of the secret service closes the door. We then see the president through a sniper's sight and the door is open. (00:12:20)
Revealing mistake: When C-Note is hanging at the start, you can see he has some protection on under his jumpsuit as his build is a lot more stocky than his actual build. (00:01:30)
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)
Answer: Don Self actually worked with Whistler before he died. And Whistler with the bird book actually knew where Scylla was.