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.
Other mistake: The psychologist shows Michael a photo of his family with his Mom, Dad, Michael and Lincoln but Michael never actually met his father when he was young.
Other mistake: While Paul Kellerman talks to Lincoln about Sofia and LJ, Dominic Purcell has a tattoo on his left forearm saying "j.c. 1950-2008", which should have been hidden as season 4 is set in 2005. (00:40:57)
Other mistake: Sarah and Michael are walking along the beach at the end. There is quite a clear path disturbed in front of them from where they practiced the shot before.
