Omissions:
I really enjoyed that they gave the prisoners a jumbo-tron to watch nature scenes while in prison. Pollux Troy also apparently appreciated the highly erotic salmon spawning footage they played. Later after Castor Troy diffuses the bomb the prison cuts to CNN to so that Troy can taunt Archer with "interception, now our side has the ball, sorry". That's kind of weird. Why would they cut to live news updates?
Also during the shoot out where they play "Somewhere Over the Rainbow" why does Adam run to the center of the room? I know he's a just kid but if there was an insane gunfight going around me the one place I'm not going to run is to the center of room and stand there catatonic. To top it off a cop shoots at that stupid kid. "Hey cop!, WTF?! You just shot at a kid."
One last note about the prison. When the zoom out and show the prison it just looks like a regular off shore oil rig. There's no way they could fit and entire prison (even a small one) on that thing. Unless the prison was completely under water and we can see it. Which seems like a lot of trouble to go to just to make a secret prison.