Revealing mistake: When C-Note leaps out of the train, you can see that the man jumping out of the train is a stuntman. He is much chubbier than C-Note (wearing a life vest) and his face is completely different. (00:22:20)
Continuity mistake: When Steadman is watching the agent put the bags that contain the remains of Veronica Donovan into the trunk of the silver car, the license plate changes between shots. The first time we see the car, the plate reads "1029Q", the second time (close-up shot as the agent closes the trunk) it reads "9417X". (00:37:20)
Continuity mistake: After Lincoln and LJ have been recognized by the waitress, they speed off down a road. During their conversation in the car, whenever we see LJ from (his) right side, his hair is blowing in a strong draft, and is blown away from the temple. In all other shots, his hair is completely calm, and is hanging down and forward, covering his right temple completely. (00:13:50)
Continuity mistake: As the train is approaching the police road block, we get a shot behind the police cars right before the train hits them. At that point all the policemen are gone. In the next shot, the policemen are back by the police cars. (00:28:30)
First Down - S2-E4
Continuity mistake: When Abruzzi is shot, he falls backwards and lands with his head pointing towards the wall of the motel. Cut to the FBI agent, then back to Abruzzi, and he is now lying the complete opposite way, with his feet pointing towards the wall. (00:36:30)
Continuity mistake: When Michael is sitting in the park he's staring at the front page of the newspaper. As the camera follows a man in the park you can see that Michael has opened to the midpages, but in the next shot Michael is looking at the front page again, before opening it another time. (00:02:00 - 00:02:30)
First Down - S2-E4
Continuity mistake: During the car chase in the beginning of the episode, Bellick's car swerves to avoid hitting a truck as they go over a bridge. The next shot is from in front of the cars, and in the background you can see the bridge and a stretch of road behind it, but the truck has vanished. (00:02:40)
First Down - S2-E4
Continuity mistake: All throughout the car chase, the car Michael and Lincoln are in has a license plate on the front bumper. But after Bellick has forced their car off the road, the car makes a jump before hitting a tree, and while it is in mid-air you can see that the license plate has disappeared. (00:02:50)
First Down - S2-E4
Continuity mistake: Bellick's partner, Geary, is wearing a light grey T-shirt, with a very prominent sweat stain on the front. Throughout the episode, this stain constantly changes shape and size, even within two shots of the same scene, and sometimes it disappears altogether. This is best seen when him and Bellick are herding the prisoners to their car. In the close-ups of him, his shirt is completely dry, in long shots the sweat stain is there. (00:04:45)
Continuity mistake: When Steadman takes out his gun, he presses it to the back of Veronica's head. She does not flinch or shy away from the gun, but in the next shot, a close-up of Steadman, the gun muzzle is pointed at the camera with Veronica off-screen, and so the gun is suddenly not touching her. (00:22:40)
The Message - S2-E15
Continuity mistake: When Mahone is on the phone with Agent Kim, Mahone's cell phone jumps back and forth from his right ear to his left ear. (00:20:20)
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)
Character mistake: When C-Note is using the woman's computer on the train, the Army website says "Access my be denied to some parts of this site" instead of "Access MAY be denied." (00:21:00)
First Down - S2-E4
Continuity mistake: Link pulls the clip out of his pocket, and the way he holds it changes between shots. (00:39:00)
First Down - S2-E4
Continuity mistake: The front licence plate disappears from Link's car as it hits the tree. (00:03:20)
Answer: Don Self actually worked with Whistler before he died. And Whistler with the bird book actually knew where Scylla was.