When Abruzzi's pilot becomes spooked as they hear the sirens come closer, he says "We've gotta go." The next shot shows the approaching police cars, and if you look closely, you can see the inmates run off to the right, even though they have not arrived there yet.
During the escape, Abruzzi says everyone will cross the wire in alphabetical order. However, after Abruzzi, the order in which everyone crosses is Sucre, then Patoshik, then Apolkis, then Bagwell, then Franklin, then Scofield, and lastly Sanchez.
The goof items below may give away important plot points.
In the part where the prisoners are throwing the toilet paper. You can see how one of the cell doors is not locked and it moves when "prisoner" grabs it (approximately 15 seconds after when warden Pope comes out of the cell).
When swearing in the VP as president, they declare her the 46th President of the United States. In 2005, the 43rd president was in office. Once the president dies she would become the 44th and not the 46th.