Factual error: Gorillas are almost exclusively herbivores. They have been observed eating small insects and grubs but nothing larger. So why does Isabelle eat a rat at the beginning of the film? The serum may have turned her into a crazed killer, as it does with Sebastian, but it hasn't changed the structure of her teeth and palate, biochemistry of her digestive system and so on, all of which would be required. She might kill or torture the rat, but she'd never eat it.
Plot hole: Why on earth would the military be interested in a soldier (sailor, aviator, whatever) who has to go into combat naked and unarmed, and who is detectable by an enemy equipped with a pair of cheap, mass-produced goggles? How would you treat them if they were injured? They would be utterly useless in any form of military operation, even espionage.
Factual error: When we first see Caine (Bacon) enter the military base, there are Willy's Jeeps used by military personnel. By the year 2000, the Willy's Jeep was long-since replaced in the U.S. Military by the HUMVEE, which we also see in the film.