Other mistake: When Michael climbs up the rope to get to the room below the infirmary, the rope is hanging from the manhole cover, but he still manages to lift the cover whilst hanging from it. In the next shot where he looks down the manhole, its clear that there is nothing other than the rope he could have held on to while lifting the cover. An impressive accomplishment, defying the laws of gravity. (00:38:00)
Other mistake: Michael goes to Fox River in April. Maricruz gets pregnant in the same month. In mid-June, when Michael get arrested in Panama, she's still pregnant. That's 2 months. He was in there for about 2 weeks, due to his deal with the company. Therefore, he would have escaped Sona at the end of June or the start of July. The start of Season 4 is set 3 weeks after the escape from Sona, so Maricruz should be 3 months pregnant, but gives birth at the start of season 4, meaning that the baby is 6 months early but looks very healthy.