Revealing mistake: When the bridge is exploding from the mine attack, the stuntman playing Jason obviously launches himself out of the captain's chair.
Revealing mistake: After Nuclear Man destroys the cab's hood, the shot changes and there's a thick string running behind him all along the car, and the cab driver is stretching out to pull it. Probably he was activating some sort of bad FX.
Revealing mistake: When the Enterprise is leaving its docking station and pulling out, two little bugs or debris from the model lands on the camera lens on the lower left corner (corrected in the Director's Edition).
Revealing mistake: Mirrors were used to make the corridors appear longer, early in the film when Brett is complaining to Parker about the way they are treated by the company you can see their reflections in the mirror behind them as they walk down the corridor. It's only for a second as they are moving off camera but you can see them in their white overalls.
Revealing mistake: When the taxi goes over the edge to capture Dr. Neville, you can see that the underbody of the car as it goes over is a flat painted surface and not the underside of what should be there (i.e., muffler, gas tank, etc.).
Revealing mistake: In the shot where Dick Jones is falling from the top of the OCP building, both of his arms appear to be about a foot longer than they should be. (01:36:30)
Revealing mistake: When the lawn mower the heroes send off as a diversion crashes you can see a wire pulling it. (01:01:30)
Revealing mistake: Underdog's first costume is supposed to be a felted down (the more accurate term would be fulled) wool sweater. When wool is felted the stitches lose clear definition and usually achieve a "felted" look. It is clear that the sweater in the movie has just been switched for another smaller sweater as the stitches are still sharply defined after it has been pulled from the dryer. This is especially clear around the U. No attempt to make the smaller sweater look "felted" was made. This refers to the original costume with the solid white U, not the second costume with the yellow outlined U.
Revealing mistake: When Stan falls into the dug-out at the baseball game you can clearly see the crash mat that he lands on.
Revealing mistake: When Ripley first burns the egg plants inside the nest, the Queen screams and moves her head. The steel rod used to hold the Queen's head to the rest of her body is easily visible.
Revealing mistake: When the Hudson Ferry captain casts off the large label that reads "Hudson Ferry" is on his left side of his jacket. However, in the exterior shot as he looks out the window at the whirlpool, the label is on his right side. This shot was flipped, and amusingly, the CGI guys actually retouched the words "Hudson Ferry" so it wouldn't read backwards. (01:02:25)
Revealing mistake: After Toad spits his slime at Jean Grey he falls to the floor. You can see the tether that was holding him in mid air. (01:13:55)
Revealing mistake: During the big underground fight scene, the solid rock wall moves as George pounds a Morlock's head against it.
Revealing mistake: When Sandman is in the truck of sand and the cop climbs up to catch him, you can see the edge of a platform uncovered. The platform is clearly there so the cop could walk without sinking - he stops right where the platform ends.
Revealing mistake: When Sarah is making her way to the baby Stego, just before she gets on her belly and crawls closer to it, you can see the kneepads she has on.
Revealing mistake: When the Enterprise is leaving space dock, look at the right (starboard) side of the ship. You can see the shape of the mounting arm the model was mounted on, even though it was blacked out to look like space, and it also blocked out the bottom of the dock. The footage was reused from Star Trek: The Motion Picture.
Revealing mistake: Each crew member has a monitor on their spacesuits that they use whenever they are exploring the caves. Whenever the monitor is shown, each crew member's individual heartbeat is shown in the lower left corner of the monitor. But no matter which heartbeat is shown, every time a heartbeat on the monitors is shown, it is always the exact same heartbeat, despite the various changes in panic and stress throughout the movie.
Revealing mistake: There is a shot right after the first time the clerics are entering the city from the nethers that you see an APC patrolling the wall road above the entrance. In that shot two shadows are being cast on the road. As the CGI APC passes through them they simply don't cast a shadow on it as they should. (00:08:40)
Revealing mistake: Near the end, as they approach LAX, the woman says there is nobody on the ground, that it's just the same as Bangor, but actually you can see a few cars moving on the ground.
Revealing mistake: When three of the turtles are playing Trivial Pursuit and Leonardo runs in to announce Splinter is alive, you can see a wire coming out of Raphael's shell. I guess it's for the animatronic head, but it's visible. (00:59:30)