Plot hole: The Kansas police arrest Bellick for, and he is subsequently convicted of, Geary's murder based in part on a threatening voice mail he left on Geary's phone. But The Message's time and date would match the records of Bellick's admittance into the hospital, thus proving him innocent of the crime.
Continuity mistake: When Steadman is watching the agent put the bags that contain the remains of Veronica Donovan into the trunk of the silver car, the license plate changes between shots. The first time we see the car, the plate reads "1029Q", the second time (close-up shot as the agent closes the trunk) it reads "9417X". (00:37:20)
Continuity mistake: After Lincoln and LJ have been recognized by the waitress, they speed off down a road. During their conversation in the car, whenever we see LJ from (his) right side, his hair is blowing in a strong draft, and is blown away from the temple. In all other shots, his hair is completely calm, and is hanging down and forward, covering his right temple completely. (00:13:50)
Continuity mistake: Season 2, episode 6. While the guys are digging in the garage, Michael tells Sucre about the website they can use, as C-Note walks in. He closes the door behind him, but misses the catch, and you can see the door start to swing open again behind him as he walks further into the room. Cut to Lincoln for a second, then to a wide shot, and the door is now firmly closed.
Factual error: Linc arrives at the 'Bolshoi Booze' location at 17:45. It is an 8 hour drive from Trinidad Colorado to that location, which is right on the Texas - New Mexico border. That means that they would have had to have left at 09:45 that morning. But they don't appear to have stayed a night at Linc's father's place - and in none of the other plot lines has it been night. They couldn't have covered that ground in the time span of the plot.