When the judge tells Bellick that his bail has been denied, Bellick puts his hand to his face twice in between shots.
When Denise and T-Bag are in the post office, a close up of T-Bag's wanted poster shows his name as being spelled "THEADORE BAGWELL" rather than "THEODORE BAGWELL."
When the camera zooms out showing Bellick in GenPop, he suddenly has tattoos on his arms, matching Michael Scofield. Michael's head has been composited replaced by Brad's, it is the same shot as the pilot.
The Alibi bar shown in the beginning is located in Hillcrest in San Diego, CA, not Kansas.