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.
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.
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 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.
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.
What is Michael Scofield's correct date of birth? On the form he fills out at Fox River in S01E01, he writes 9 August 1978. When Lincoln finds the photo their mother left for him on which she is pregnant with Michael, he says, "It's been doctored. That's a 78 Zephyr. Michael was born in 76". Finally, it's 10 August 1974 on Michael's tombstone in S04E22. The date of death on the headstone of Sara's father, who died way earlier, is 1 June 2005 (S02E18), whereas Michael's says 11 April 2005.
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.
In a season two flashback, Michael remembers when he once visited Lincoln in prison. He says Lincoln had killed the President's brother, but at the time when Lincoln was charged with the murder of Terrence Stedman, he was only the VICE-president's brother, as mentioned on many occasions in the first season. The VP was only promoted to President much later on in the series. This may have been to prevent confusing people who had not seen the first season. The newsreaders in the show referred to Terence Steadman as the 'President's brother' and a flashback saying he was the VP's brother may have caused some confusion.
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.
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.
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"
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.
Micheal's escape plan was more complex. They dug the hole under guardians room and they passed through the asylum in order to reach infirmary. Yet, during riot, Micheal had reached the infirmary by passing only pipes.