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.
When Lincoln and Sucre are in a standoff with a Company agent that is holding Sofia hostage, the silencer appears on the agent's gun between shots.
If you look closely while watching Scofield change his shirt you can see the scar from the pipe burn in Season 1 on his right shoulder. Because of the tattoos it is a little hard to see.
When Whistler is fighting on the roof with Scofield the rope hoist is visible before the helicopter is actually shown lowering it.
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.