When T-bag shoots Bellick in the leg on the fire escape, the scream used in the audio is the same scream that Michael uses when Sucre rips the guard uniform off of his burned back in Season 1.
When Michael arrives at Fin Del Camino, he has several flashbacks of T-Bag. One of these, from episode 1.12, "Odd Man Out", is of him slashing Abruzzi's throat. But not only was Michael not present for this, Abruzzi never told him that T-Bag was responsible for it.
When Lincoln points the gun to Agent Mahone after they fight, he says "Toss me the handcuffs..". Afterwards, we see a flashback to that scene. In the flashback, Lincoln now says "Give me the handcuffs..".
When the fire alarm is pulled at the hotel it says "Atención damas y caballos". Caballos means horses in Spanish, it should say caballeros or gentlemen.
In a Mexico City landscape you can see BITAL. In fact that is the name of a Mexican bank that disappeared in 2004. Is obvious that they used and old film footage.
On Paul's Army dress uniform, his rank was Lieutenant Colonel. Given his age, he would not have had time to achieve such rank in the Army, as well as, his high standing in the Secret Service. Additionally, he was wearing a green beret with a Ranger scroll. This is completely incorrect. The Airborne tab is missing, as is the Ranger tab, and a Ranger would have a tan beret. If he were a green beret, he would have the Special Forces tab, along with the Ranger tab (since he's an officer) and Airborne tab, but no scroll.
When Mahone is pretending to be Sucre and intercepts the messages from goldfinch.net you see that he reads the following line: "I'm in. Let me know when you get there. Michael" but on the actual form in real life it just says: "I'm in. Let me know when you get there." So without "Michael".