When Abruzzi walks into the hotel room to kill Fibonacci, he shuts the door behind him. When the FBI shows up and Abruzzi is inside the hotel talking to them, the door is open.
During the chase scene at the start with Bellick and Scofield, the passenger side headlight on Bellick's car changes from broken to unbroken.
In the chase scene at the start with Bellick and Scofield, the car was Chevrolet caprice 1977, when they stopped, the car became Chevrolet caprice 1986 and still as that till the end.
When Nika Volek threatens Michael Scofield and Lincoln Burrows at gunpoint, she says that she would get $200,000 for turning them in but it was previously established that she would get $400,000 as the reward for the capture of Lincoln Burrows was $300,000.