In this episode, Sammy wants Cristobal and his men to join Lechero's gang. One of Cristobal's men (the shirtless one) was seen in Lechero's gang in episode 3.1, "Orientación", when he was seen walking with Sammy and Lechero while talking about Michael's fight. In this episode, Lechero acts as if he doesn't know him.
At a certain point we see Michael and Whistler hanging on a rope below the Helicopter. A few seconds later someone in the Helicopter gets shot and falls down, at the point where he passes the part where Scofield and Whistler should be hanging, they are not there.
(at around 36 mins) The prison is said to have no air conditioning. However, when Whistler is on the roof of Sona during the attempted escape via helicopter, two industrial sized air-conditioning units are clearly visible on the right-hand side of the screen.
The goof item below may give away important plot points.
When Lechero first opens the door to the tunnel, the door swings to the left when it opens (hinges on left). But when they come back out, Michael closes the door that would swing right when opened (hinges on the right). Then the door swings left again when Michael and James enter through the door again.