When Kellerman, Scofield, and Burrows escape from the tunnel in Albuquerque they take off in a Chevrolet Suburban SUV, but when they arrive at the airfield the vehicle is a GMC Yukon SUV although of the same colour and class.
Most of the main characters committed crimes in different states. (T-Bag in Arkansas, Fernando in New York, etc.) However, they are in a state prison in Chicago, not a federal prison.
Lincoln is often seen speaking with Michael in the yard or on a work detail. In reality, Death Row inmates, RARELY leave their cells, are not given work details, and never interact with General Population.
Dr. Sara Tancredi keeps giving Michael insulin shots using a regular syringe. Insulin syringes are several times thinner with short needles, which is why no diabetic prisoner in the USA goes to a prison doctor for his insulin shots 5-6 times a day. Moreover, she keeps giving him intramuscular shots of insulin instead of hypodermic.
Micheal's escape plan was more complicated than it needed to be. They dug the hole under guards room and they passed through the asylum in order to reach infirmary. Yet, during the riot, Micheal had reached the infirmary by passing only pipes.
In the opening credits, there is a set blueprints shown on the right side of the screen. One line states 7' 15" and another says 23' 15", there are only 12 inches in a foot, the true measurements would be 8' 3" and 24' 3"
Michael says that he chose Panama because there is no extradition treaty. Based on the date on Sara's father's tombstone, 1 July 2005, Michael was still incarcerated on 8 May 2005 when the United States and Panama entered into an extradition treaty, explaining why he would be unaware that the brothers could be extradited.
The two brothers and the other convicts are all going for the D.B. Cooper's five million, which was stolen several decades ago. There are design changes in the US Dollar bills so how are they going to use the buried five million? While there have been several design changes to US currency, this does not mean the money cannot be used. It is still considered legal tender. However, money taken in the D.B. Cooper heist just showing up all of a sudden in circulation would be a little eye-brow raising.
The toilet in cell 40, which is eventually Michael Scofield's cell, has no pipes for the waste exiting or water entering his cell. This toilet could actually not be used.
In multiple episodes during season 1, when Michael is in his cell removing the toilet, he appears to be removing the Allen head screw from the side of the toilet with his fingers, yet there is clearly an empty screw hole and no screw present.
The series takes place over a 1 year period, all in 2005, yet the model of Cadillac Escalade being driven is at the earliest a 2007 model.
An audio recording on a USB flash drive is referred to as a tape.
When the show cuts away to "Blackfoot, MT" it often shows a mountain range. The range shown is actually the Tetons, featuring Mt. Moran, which are located in northwestern Wyoming, not in Montana.