Plot hole: Spyro says to Rafael the gun dealer that they need the "hardware" (guns) cause they're going to be hit, but in the scene before we see the Diablos already hitting them after the Mayor finishes talking to the police over the phone.
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.