Continuity mistake: They are hanging on the helicopter's rope, then they're still fighting on the roof and the helicopter's rope is being lowered. (00:37:50)
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)
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: In the shot where Scofield and Whistler are clinging to the wire from the helicopter, one of the bad guys gets shot and falls out of the helicopter. He falls past the wire, but they're not hanging off it. (00:38:35)
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)
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)
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: Lechero regains command of the prison and dumps the bodies of the two guys off the ledge. His face goes from being clean to full of sand to clean in three short shots. (00:36:20)
Under & Out - S3-E11
Continuity mistake: When T-Bag and Lechero are in the tunnel talking about Michael planning something, Lechero has the crowbar level with his face in some shots and lowered in others. (00:14:00)
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)
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
Revealing mistake: When Link is dabbing Sofia's burns its clear to see he's not actually making contact with her. Just making the motion. (00:26:10)
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
Plot hole: Gretchen, Lincoln, and Sophia were able to visit Scofield and Whistler in Sona without Gretchen being recognized. She was taken in for questioning in episode 9, but she managed to escape and kill General Zavala and one other guard. The other guards knew that she was the one who killed Zavala but she was still able to sign in for visitation.
Answer: Don Self actually worked with Whistler before he died. And Whistler with the bird book actually knew where Scylla was.