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.
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 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: 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)