Continuity mistake: Alexander Mahone reveals his so called past to Tweener and shows pulls out 2 pills from his pen, however next time we see the pills there are 3. (00:12:10 - 00:13:20)
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 Sara Tancredi is pulling her dead father off the door he lets out a very audible grunt and you can see his eyes and mouth moving around, a few seconds later he is on the floor and his eyes are dull and his skin slightly pasty. (00:16:40 - 00:17:05)
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)
Continuity mistake: Tweener is talking to his lover then has his arms up on his head, then the FBI catch him and tell him to put his hands up. (00:34:36)
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)
Continuity mistake: You can see David with his hands behind his head, but in the next shot he still has his hands beside him, and only later places them behind his head. (00:34:48)
Character mistake: Mahone is very smart and meticulous, similar to Schofield. He has a good knowledge of forensics as shown throughout the show. However he shoots Tweener, and places the gun in his hands after shooting him. He would know that the blood on Tweeners hands would show he wasn't holding the gun when he was killed due to blood spatter behind behind the weapon. (00:40:20)
Answer: Don Self actually worked with Whistler before he died. And Whistler with the bird book actually knew where Scylla was.