Revealing mistake: When they get on the boat you can see the outline of the wetsuit under Michael's shirt. (00:27:20)
Continuity mistake: At the Buoy, McGrady's hair is constantly changing between shots. (00:21:40)
Revealing mistake: When running to the stash on the beach you can see tracks from previous takes. (00:15:30)
Continuity mistake: When Bellick is being choked, the guard's arm is constantly changing position around his neck. In some shots, Bellick's neck is in the guard's elbow joint, and in others it's halfway down the guard's forearm. (00:07:45)
Under & Out - S3-E11
Continuity mistake: When Link is dabbing Sofia's burn marks, the dressing changes from his left hand to his right hand instantly. (00:26:10)
Under & Out - S3-E11
Continuity mistake: The truck in no man's land comes to a stop next to the tunnel. Camera changes and now it's a good 4-6ft away. (00:15:10)
Under & Out - S3-E11
Continuity mistake: We see the truck approaching the tunnel in no man's land. In one shot from the truck, it is by a massive puddle. Camera cuts to a wide shot, and the massive puddle has gone. (00:14:50)
Good Fences - S3-E4
Revealing mistake: When we see Sucre cutting the passport photo with a scalpel, the blade doesn't cut the picture, it instead moves it. However Sucre acts as though he has cut the picture.
Call Waiting - S3-E3
Continuity mistake: When Bellick is talking to Pistachio, Pistachio pulls out the razor and starts to close it. Camera changes and she closes the razor again.
Audio problem: Agent Lang tells Mahone he has to go back to Sona, in the over the shoulder shot her mouth doesn't move but she can be heard talking. (00:40:00)
Visible crew/equipment: After Michael has dropped back into Sona we see him running away from the camera with a nice big camera shadow on his back. It's nothing in the surrounding area. (00:38:30)
Continuity mistake: We see Whistler grab hold of the hand rail while stood on the roof. As Michael grabs him however less than a second later he is around 4ft off the floor. (00:38:00)
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)
Answer: Don Self actually worked with Whistler before he died. And Whistler with the bird book actually knew where Scylla was.