When Mahone is pursuing Sarah and Michael in his car (before they crash), close-up shots of Sarah show her holding onto the handle in the roof of the car for dear life. This is in every close up shot. In every shot where you can just see their outlines in the car from far away, she doesn't have her arm up.
After Michael traps Mahone in the warehouse, he walks out to Sarah's car, where she is waiting for him. Her hair is up and messy. When Michael finishes walking around the car to get in, her hair is down and smooth again.
When Lincoln and LJ get caught the Willcox, Arizona police, they are transported in a 1998 Ford Crown Victoria, and when the police car gets rammed by the black van, the car's rims are different.
When Geary beats down Bellick in order to get Westmoreland's money, we see a newsstand in the background. It is labeled with "Willcox News". However, Geary and Bellick are supposed to be in Tribune, Kansas, and not in Willcox, Arizona, where Lincoln and LJ have been apprehended in the episode before.
When Sucre leaves the message for Maricruz, he tells her that his aunt in Mexico has a llama. There are no llamas in Mexico, llamas only live in the Andean countries of South America.
Michael never knew what name Sara would use to get a hotel room. Yet he faxed a mail to Sara without knowing her name nor her Room Number. Later receptionist at the Sundown hotel asks Mahone if he was the one who tried to contact her.