When the car that Scofield and Burrows stole from Bellick is seen as they pull into the town in Utah, the headlights are clearly intact. In the episode before, when Bellick ran Scofield's previous car off the road, the right headlight was broken out due to the damage sustained in running the car off the road.
As C-Note jumps from the train, you can see the buoyancy aid being worn underneath his clothes.
When the FBI agents are searching Michael's hard drive, it shows all of the newspaper articles that Michael used to help plan his escape. However, in the earlier episodes when these articles are shown, they are articles clipped form newspapers, definitely not printed off the computer. So why would they be on his hard drive?
When C-Note uses the laptop to login into a US Army server to search for the K K Ranch, it gives the location as Tooele, Utah. The GPS coordinates N 43o 46' 45.9'' - W 111o 38' 35.5'' are in reality way off Tooele, Utah (some 350 km off).
After Michael and Linc return to the car, Tweener inquires if the money will be split equally. Linc says Tweener isn't worth 1.5 million dollars, but one-fourth of 5 million is only 1.25 million.