Continuity mistake: When Sophia walks out of the hospital with Lincoln she has blood drips down her right side of her shirt. After Susan tells her to go home the blood is down the left side of her shirt. (00:04:00 - 00:05:00)
Continuity mistake: They show Michael changing his shirt and you see his tattoos on his back, but for a split second you can see his stomach and it doesn't have any tattoos. (00:39:55)
Continuity mistake: When the raid starts we see a pickup explode and the bonnet flying off. Camera cuts and now the bonnet is suddenly lying on the floor. (00:35:50)
Interference - S3-E5
Continuity mistake: After the raid, Lechero has his hand on his woman's elbow. Camera changes and now it's on her face. (00:35:20)
Interference - S3-E5
Continuity mistake: When the guards leave the prison, one has his gun raised by his head. Camera cuts and now it is down by his side. (00:33:20)
Interference - S3-E5
Continuity mistake: When Tyge is washing and Bellick talks to him, the rate of which the water is flowing changes from a trickle to a torrential blast and back between shots. (00:11:25)
Interference - S3-E5
Continuity mistake: When Link is discussing the road with Sofia he has his hands on the map in one shot and one up to his mouth in the next. (00:08:45)
Good Fences - S3-E4
Continuity mistake: When Mahone corners Michael in his new cell, he stabs the knife into the wall. Between shots, Mahone's grip on the knife is constantly changing. (00:39:15)
Good Fences - S3-E4
Continuity mistake: T-Bag kills Nieves and takes the bag off his head. Camera changes and his fake hand is now over Nieves' throat. (00:30:10)
Good Fences - S3-E4
Continuity mistake: When Lechero walks out in to noman's land and orders Michael into the hole, he is buttoning his shirt up. When the camera changes his hands are by his side. (00:26:50)
Good Fences - S3-E4
Continuity mistake: Michael asks Link to reach out to the gravedigger. When he does he is holding the fence in some shots and not in others. (00:03:50)
Good Fences - S3-E4
Continuity mistake: When Michael is seen walking to watch the grounds keeper at the start, the sweat patch on his back changes size and darkness between shots. (00:01:30)
Call Waiting - S3-E3
Continuity mistake: T-Bag walks in on Lechero who has his hands up to his head. Camera changes and his hands are down. (00:36:20)
Call Waiting - S3-E3
Continuity mistake: Whistler goes to talk to Mahone in his cell. Mahone alternately has his hand by his mouth or lowered. (00:28:00)
Call Waiting - S3-E3
Continuity mistake: When showing Whistler the picture of Sara, the way it's held changes between shots. (00:16:30)
Fire/Water - S3-E2
Continuity mistake: Mahone holds a steel pipe out in front of him as Lechero walks towards him. As the camera cuts the bar is now held behind his head. (00:35:20)
Fire/Water - S3-E2
Continuity mistake: When Michael is talking to Link about having found Whistler, his grip on the chain link fence keeps changing. In some shots his hand is shoulder height, in others it's over his head. (00:15:00)
Fire/Water - S3-E2
Continuity mistake: The phone Link has when showing Michael the video changes designs between the front and rear shots. Note the antenna. (00:40:30)
Orientación - S3-E1
Continuity mistake: The way Gretchen holds her martini glass when first talking to Lincoln shifts during camera angle changes. (00:36:45)
Orientación - S3-E1
Continuity mistake: When Michael is swinging the foot in his cell, the string is over his middle finger. Camera changes and it's now only over the index one. (00:31:00)
Answer: Don Self actually worked with Whistler before he died. And Whistler with the bird book actually knew where Scylla was.