Plot hole: There must be a lot of dumb scientists in Sebastian's lab. While defibrillating the invisible gorilla, (s)he becomes completely visible for a moment. However, not once do the scientists consider that applying a mild electrical shock to the system renders the invisible animal visible again - that electricity may be the key to the whole invisibility problem. They don't even comment upon the fact that the gorilla does become visible.
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: Rats have very poor eyesight but an extremely keen sense of smell. The rat introduced into the gorilla's cage would know right away that there was another animal in the cage and would never scamper happily into danger, as this one does.
Factual error: When they put the gorilla back into the cage in the movie, who is said to be female several times, you can spot that it has a silver back. Female gorillas do not ever have silver backs - it's strictly a male thing.
Continuity mistake: When they try to make Kevin visible, they use a blue spray to see his vein (like they did to the gorilla). but you never see the blue mark again...
Factual error: When the crew pour liquid latex over Sebastian's head and neck, in order to create a fairly life-like mask of his face, it simply pours over his head as though he is completely bald, and he is able to remove it later by pulling it off, exactly like a glove. However, the film creators seem to forget that Sebastian has quite a thick head of hair, and technically, when they pour the latex over his head, it should stick and/or pour along the outline of his hair. Whilst drying, the mask should equally have stuck to his hair and become very difficult to remove, and yet as they create the mask, no hair appears to exist on Sebastian's head. They did not shave Sebastian's head - later in the film he falls into a swimming pool and we see a clear outline of his entire body, with a full head of hair. (00:47:15 - 00:48:30)
Continuity mistake: When the veterinary is throwing blood to stain Sebastian, she stains her left breast. A few seconds after, there's no stain.
Factual error: When they inject the serum that counters the invisibility into the gorilla, you see the serum flow backwards toward the gorilla's hand. Veins have special valves that prevent blood flow from going backwards and to force blood to go to the heart, so how the serum manages this is beyond me.
Factual error: When they make the gorilla visible again, her heart becomes audible at the same time it becomes visible. This happens with Kevin Bacon as well. But that shouldn't happen, because it was just invisible, not inaudible. And it wouldn't make a noise like that unless you were listening through a stethoscope.