Revealing mistake: During the nighttime forest fight-scene, when the Zoanoid rips the tree out of the ground, it's obviously a lightweight prop. Furthermore, when he starts trying to swing it at the Guyver, both ends of the tree are broken off cleanly... which doesn't make sense since the top half should be covered in branches and whatnot.
Factual error: The drug-runners at the start of the film mention that their scheme is to smuggle cocaine by mixing it with molten plastic, molding the plastic into dolls, shipping them and then re-melting the plastic to separate the cocaine again, which will leave it "100% pure." While you can indeed smuggle cocaine by mixing it with plastic, the process to recover it is way more intricate than simply re-melting the plastic, and requires chemists to treat the plastic with all sorts of chemicals and compounds in a complex process (and it will not be "100% pure" as suggested), and it is usually done with larger plastic objects (like plastic dog-houses or car-parts), as something the size of a doll isn't going to be able to hold all that much cocaine.
Revealing mistake: When the security guard is killed near the end of the opening scene, watch when he gets shot... you can see small flashes/sparks going off on his chest from the squibs at least twice.
Character mistake: A character mentions carbon-dating one of the fossils found. This is preposterous... you can't carbon-date fossils like the ones being shown. Radiometric dating maybe... But certainly not carbon dating. He's a professional and should know more than better that carbon dating wouldn't work.
Revealing mistake: During the final battle, at one point Crane picks Sean up by the neck and kicks him in the side, sending him flying onto a nearby rope bridge. When the camera cuts and you see Sean hitting the bridge, watch closely... he's coming from a completely different angle than the one Crane kicked him in. In the first shot, Sean is kicked diagonally towards the bridge from about a 45 degree angle. In the next shot, it's clear the stuntman was standing at the edge of the bridge and just jumped forwards to land. It goes by quick so you might not notice it the first time, but it's there.
Deliberate mistake: During the final battle, at one point Sean kicks Crane off a rope bridge. When this happens, if you look closely you can see the rope railing on the side of the bridge fall away right before Crane falls. It's supposed to look like Crane is falling through the ropes, but they drop just a split-second too early (he's not even touching them when they start to fall), so it was done on purpose and mistimed. (It was likely timed to drop away just a split-second before Crane fell so that the stunt-person wouldn't accidentally get tangled in the ropes as they fell).
Audio problem: During the final battle, when Sean and Crane start fighting with their arm-blades, listen closely. There's just a few too many "blade clashing" sound effects added in, and it doesn't always perfectly match up to what's on-screen. More were obviously added in to make it seem more dramatic, but it doesn't quite seem "right" if you pay close attention.
Revealing mistake: In the final battle, at one point Sean gets kicked through the boards on some scaffolding, which in turn makes the whole thing fall over dramatically in slow-motion. When Sean flies through the boards that are holding the scaffolding up, however, they way they break and react reveals that they are cheap, light-weight breakaway boards. They break like nothing, don't splinter at all and before the shot cuts, you can even see them wobbling and shaking like they're made of styrophone.