Plot hole: When they rescue the boy he is with Gary Sinese. Surely the boy could hear his voice and tip off authorities he was one of the bad guys? Yet later in the movie when Sinese comes by the home for his reward, he hears Sinese's voice and recognizes it.
Plot hole: In the scene after Gil saves Bobby's son Shawn, Gil claims he doesn't know who Bobby is. Even guessing that he may be Barry Bonds. Then in the next scene when Gil is pitching to Bobby he knows all about his slump, number, contact, and about Primo's death and this did not strike him as odd?
Plot hole: Malloy and the others tell Snake that the Plutoxin 7 virus would cause nervous system shutdown without the antivirus. When he got back, it was revealed that it was just a hard hitting case of the flu. Why then did, at the base, the computer showing his countdown timer over the course of the film say when nervous system shutdown, not the full extent of the flu, would occur. Maybe for sake of the audience to avoid a spoiler, but those who had already seen the movie would notice this.
Suggested correction: Because the countdown timer was lying to him as well. It was programmed to do so.