Factual error: Amongst the essential parts of a nuclear weapon's detonation mechanism is a radioactive isotope of tritium, which has a half life of just 12 1/2 years. The tritium in every nuke on earth has to be replaced every ten years or so. This is by no means unusual; there are other perishable parts including detonators made of conventional explosives which would be completely inert after a thousand years. After lying dormant with no maintenance at all for that amount of time the nuclear weapons the 'Man-animals' find would be big shiny paperweights and not much else.
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: Peter goes into Carl's mind to save Catherine. When he's in there he sees the tank with the water nymph. On the tank are strange symbols which provide the FBI with the clue needed to find the latest victim. Makes sense so far. But, go back to the scene just after the FBI have captured the comatose killer and are looking in his basement. The FBI are looking at the contraption that the killer uses to suspend himself over the victim. On the contraption is the same symbol seen later on the water nymph's tank. Why didn't the FBI follow up the symbol then?
Factual error: Gary Sinise looks at a computer screen with a short section (about two full twists) of DNA on it and proclaims that "This DNA looks human." He could have been looking at DNA from any single-celled organism and it would have looked just as human as what he was looking at. All mammals have 90+ percent of their DNA in common, he would have to have sequenced the entire DNA strand (something like 3 billion pairs of nucleotides) to identify it as human, something that would be totally beyond the capacity of anything but a well-equipped genetics lab, something they show no sign of having.
Continuity mistake: When Wolverine crashes into the tree knocked over by Sabertooth, notice that the entire front of the truck gets completely folded up and the windshield breaks into a thousand pieces. In the next frame, Wolverine gets thrown through the unbroken windshield and the front of the truck is practically undamaged... (00:18:05)
Other mistake: When Sugimura is looking for Kotohiki, he activates his scanner to see if she is nearby. The scanner shows her location, but fails to show either Mitsuko or Kiriyama, who show up quickly after.
Continuity mistake: After mowing down all the Immortals during the Sanctuary scene, one Watcher tells another to take their heads because they might be Immortals. You see the Watcher to the left side of the screen and a robed figure to his left about four feet away drawing his sword. Suddenly, that same robed figure is now to the Watcher right side and about two feet away.
Character mistake: When the biologist guy talks about writing code for DNA he names the four codes as A, G, T, P, when they are actually A, G, T, C.
Continuity mistake: Near the end of the film, Adam and his clone make a jump for the helicopter to escape the explosion. In one scene, you'll see Sport Jacket Adam holding the ladder to the helicopter with Leather Jacket Adam holding onto the legs of the first Adam. After a cutaway scene, you'll see these two have switched places (Leather jacket on ladder, Sport jacket on bottom). The next time you see them, they're switched back in the correct order. (01:52:30)
Revealing mistake: While the guys are going for their physicals, there's a scene in which blood is drawn and you can clearly see the tube connected to the end of the syringe pumping fake blood into the container.
Continuity mistake: At the end where Nick and Kaela swap eye colour, Nick's blue eye switches positions from right to left.
Continuity mistake: During the scene where Akima gets out of the shower, we see Cale going over some of the stuff she collected that's sitting on her table. On it there is a baseball and a picture frame that's lying flat on the table. Cale picks up the baseball, says something to Akima and puts the baseball back down on the table, where it rolls over the picture frame as if it was flat as the table.
Continuity mistake: When Leslie Nielsen came back from robbing the guys house the man who lived in the house came over to Leslie & started to talk. Later on Leslie put some blue paint on the man. When the camera angles change, parts of the paint splashes are missing on the right side of the man's chest.
Deliberate mistake: You might be wondering where Terry suddenly comes up with Jolly Jack all of the sudden after escaping the lab. In the commentary, they say that the Joker, in his transmission to Terry in the lab, was supposed to be eating out of a candy jar with "Jolly Jack" on it, but couldn't have it due to time constraints.
Plot hole: When Captain Towers gives his XO an injection to allow him to die in peace, he, properly, swabs the site with alcohol, and slips the needle into the vein. However, immediately below the injection site, is a hep-lock.a port installed into a vein to allow injectables to be administered. I cannot imagine that a senior Naval officer would be so ignorant of the port's function.
Continuity mistake: When Marci escapes from the web in the elevator shaft, she closes the door on the spider chasing her. In that sequence, the door closes automatically; in other scenes, the door opens and closes manually.
Continuity mistake: In one scene we see a police officer investigating his colleague's disappearance. In the long shot we see him walking towards the other police car and it can be seen that the number plate is a fake. A fake paper number plate has been placed over the original number plate. When the wind blows you can see the side of the paper blowing in the wind. (01:16:05)