- Continuity: Wooden chairs on deck vanish before the Nautilus submerges.
- Incorrectly regarded as goofs: It is clearly established that the movie is set in an "alternative universe" and its geography and history must therefore be as the moviemakers describe. There could be graveyards in Venice and the roads could be extensive enough to allow Tom Sawyer to drive around. In addition, the inhabitants of Venice might have been celebrating the Carnivale in 1899. (In actuality, the Carnivale was banned by Napoleon when he invaded Venice in 1797 and not reinstated until 1980.)
- Incorrectly regarded as goofs: The spelling "Quatermain" appears in the movie's credits and promotional material (as well as the original novels and the comic). However, on the grave marker of Quatermain's son, the name is spelled "Quartermain". However, this might be intentional since the writer/creator of Allan Qua(r)termain sometimes changed between the two ways of spelling it.
- Continuity: As Mrs. Harker lays on the bed in the Fantom's hiding place the position of her hair on her shoulder/chest changes between shots.
- Crew or equipment visible: During one of the attack scenes in the Nautilus, the whole ship shakes and topples to the left. While the tables in the room "slide" to the left, the strings pulling them can be seen clearly for several seconds.
- Crew or equipment visible: When the three remaining assassins dodge Quatermain's bullets in the Kenyan club, several cables can be seen hanging from their long coats all around them on the floor. These cables set off the pyrotechnics used to simulate bullets sparking off their metal vests.
- Continuity: At the end of the fight between Mina Harker and Dorian Gray, we see that Mina runs Dorian through, and we see him from the back, but we do not see the blade protruding from him. The blade and blood were intentionally left out because executives feared it would give the movie an R rating instead of the PG13 they wanted. Further, Mina pushes Dorian to the wall, leading him with the sword, we see the blade is somewhere in Dorian's lower right ribs. But when she backs away from him to get his painting, the sword is located higher in his upper sternum.
- Continuity: In the initial shot of Sanderson Reed entering town we see a long shot of the buggy on the road with no other buggies in view. As his buggy pulls up, another buggy passes, yet there were no others on the road.
- Incorrectly regarded as goofs: While Bram Stoker's vampires are not fond of sunlight, they are not adversely affected by it in the spectacular ways invented by writers of movie versions of the Dracula story.
- Continuity: When M shows the captured Sawyer to Quatermain in the reflection of his mask/helmet, the image is not reversed; the knife is still in the captor's right hand.
- Factual errors: Huggy Leaver's character is incorrectly billed on the credits as "Hanson Cab Driver". The correct term for this mode of transport is "hansom cab".
- Continuity: When M is running away from the castle, before Sawyer shoots him, the box he's carrying starts in his left hand, switches to his right, then is back in his left hand when he is shot.
- Continuity: In Kenya, the last assassin to be shot by Quatermaine is dragged back into town. Between being thrown on the ground and committing suicide, the people around him move, and appear and disappear between shots.
- Incorrectly regarded as goofs: In the final scene between Mina and Gray, Mina's hair is very curly and hangs loosely down her back at the beginning of the fight, but when she gets up from the bed to stab Gray, her hair is in a half ponytail and very long and straight. Also, she's wearing less blush during the end of that scene from she was wearing in the beginning. The Director's commentary says that this was an intentional change. They have Mina Harker's hair become curly and wild to mirror her vampiric outbursts, when she is being calm her hair is straight to reflect this. The same goes for the blush.
- Revealing mistakes: When Dorian Gray offers Mina Harker the small glass of alcohol she is to take, she reaches up with her hand. Moments later, he will smash the glass and cut her fingers, but the blood is already on her hand as she reaches to take the drink.
- Continuity: When the League are seeing Mina Harker bite her first victim in the library, the shot of Dorian Gray close up is reversed. His hair is parted the wrong way over his head.
- Continuity: When Mina finishes attacking her victim in Dorian's home, her hair is down with her running attempting to push it up. In the time it takes Tom Sawyer to deliver a single line - her hair is in a bun and her arms at her sides.
- Continuity: When Mina finishes attacking her first victim in Dorian's home, her scarf appears draped over her left shoulder. In the next shot you can see her from behind but the scarf is hung in front of her. It switches back again in a following shot.
- Continuity: When Fantom is escaping from Quatermain, he throws down his mask, but in the next shot of him escaping out the window, he has his mask back on.
- Continuity: When Mina attacks her first victim in the initial action scene in Dorian's house, she picks her head up, and messy, smeared blood is clearly visible all over her face. In about 5 seconds, all the blood is completely clean just by her running her finger over her lips a few times.
- Revealing mistakes: When the planted bombs aboard the Nautilus explode, the characters in the 'Conference Room' are thrown to the left by the force of the blasts. The cast were simply meant to fall to the left as if the room had tilted suddenly - they all do this except Dr Jekyll/Mr Hyde who falls to the right.
- Miscellaneous: In the very beginning of the movie when the tank is about to go into the front of the Bank of England the top of the door cracks before the tank goes through.
- Revealing mistakes: When the bombs aboard the Nautilus explode, the conference room's table slides from left to right. However, it is possible to see a set of strings attached to its legs pulling it across the room.
- Factual errors: Captain Nemo's Nautilus is shown traveling in one of the canals in Venice. Venice's Grand Canal has an average depth of seventeen feet, and no ship the size of the Nautilus would have a draft shallow enough for that.
- Revealing mistakes: In the Kenyan bar fight, Quatermain pushes one of the armored men into a rhino horn on the wall. The horn goes straight through the man's back and comes out of his chest. This should not happen as the armored vest should have blocked the passage of the horn.
- Revealing mistakes: When Mr. Hyde struggles underwater to open a hatch to drain the flooding Nautilus, he lets out a scream, but no bubbles come from his mouth and the sound is as if he was above water.
- Miscellaneous: On the Nautilus when the League is getting the transmission from Skinner, (the Invisible Man), After he says "Hello my freaky darlings," In the background, you see Dr Jekyll smiling and rolling his eyes. In the commentary, he explains that they all had "the giggles" that day and that was the only time that one person laughed so they used it in the film.
- Revealing mistakes: At the first jump that Hyde makes over a rooftop, he disapears before he hits the roof, and dust rises before he would have hit it.
- Revealing mistakes: When the soldier comes up behind Sawyer, you can see that the soldier is lighted the wrong way. When Sawyer hits him, you can see that Sawyers face is disfigured. In the commentary, it is explained that originally the soldier was a little girl and they changed everything by computer. Therefore, Sawyer did no acting in this part.
- Miscellaneous: In the fight scene with Tom Sawyer and the invisble Sanderson Reed, Reed is kicked and is thrown into a door which breaks apart unrealistically and seemingly skips frames.
- Revealing mistakes: During some of the head shots of characters in the scene on the bridge of the Nautilus, the sea behind them is frozen in place; no waves, no light off the water.
- Revealing mistakes: In the scene where Mr.Hyde grabs a door as a shield from bullets before any bullets hit it there are already bullet holes in it. This is pointed out by the producer on the DVD commentary
- Continuity: The level of make-up on Skinner's face throughout the movie changes. In some parts you can see that the back of his head is invisible, and in the next close up scenes of him talking you see make-up covering his entire head. This is most noticeable right after Quartermain meets Skinner to the point where Skinner splashes himself with alcohol in Dorian's home.
- Factual errors: Hanging on the wall in the bar behind Quartermain in Kenya is a Union Jack. It is the wrong way around where the red diagonal bars should be 'left-hand down' and 'right-side up' when hung on a wall. This glaring error would have been noticed more in the period that was depicted in the film but is now a common mistake.
- Revealing mistakes: We should at NO POINT see Skinners eyes, but we do during all close ups. When there is a medium shot, showing the partial make up, his eyes are gone, when there is a close up, they reappear. Unless he applies make up to his eyes as well,making himself blind, his eyes would always be invisible.
- Continuity: In Africa, you can see all the assassins have thick metal armor on. However, when Alan pushes one of them onto a Rhino's horn, is goes straight through him as if he wasn't wearing any.
- Continuity: The sailors on the sinking Nautilus turn both handwheels on the engine room door to seal it, but Jekyll only turns one handwheel to unseal and open it.
- Continuity: When Hyde first transforms into Jekyll, before he collapses on the floor his pants are the right size for his Jekyll form. When he gets up, he has to hold up his now Hyde-sized pants. Later, when Jekyll transforms in the engine room, his pants and shoes remain intact even though his Hyde form is so much larger.
- Continuity: When Quartermain is shooting off the Nautilus, the number of balls sitting beside the crewman does not change. Indeed, more appear during his conversation to Sawyer.
- Factual errors: Mina Harker taps a test tube with a yellow substance in solution and announces it to be Magnesium Phosphorous. That is an incorrect name for the compound formed by these two elements. Since it is yellow it would be Magnesium Phosphate.
- Revealing mistakes: While the League waits for Skinner in the frozen wasteland, nobody's breath is visible. This is especially telling for Skinner when he arrives, as you can see the outline of his body from the fallen snow but not his breath when he speaks.
- Factual errors: Without immediate, modern Emergency Medical Services, Skinner's burns would be fatal in only a small amount of time.
- Errors made by characters (possibly deliberate errors by the filmmakers): Quartermain and Tom Sawyer are told to make a right at the column. Tom Sawyer says which column. Quartermain says to follow him. From our perspective he goes to the right but since they are walking towards us they actually turn left.
- Factual errors: During the Arctic sequence, while the "Gentlemen" are traversing through the snow toward shelter, the Invisible Man is invisible, and therefore must be completely naked and barefoot. The footprints left in the snow by the character are shoe prints.
- Factual errors: In the Arctic sequence, the invisible man is completely invisible while the characters walk through the freezing snow. As he was invisible, he was completely nude. Somehow, he does not freeze to death.
- Plot holes: After reaching the Arctic cave, the Invisible Man is suddenly completely clothed, with his make-up, glasses, and shoes on. He walked to the cave nude, neither he nor any other character appears to be toting these items.
- Errors made by characters (possibly deliberate errors by the filmmakers): The sight of a drop of blood is enough to stimulate Mina Harker's vampiric blood lust. Yet after a disaster, she is clearly nursing injured men and is surrounded by blood, yet remains calm and maternal.
- Factual errors: The Dorian Gray's picture is much too big to fit in the space on the wall in his house.
- Continuity: During the fight between Mina and Dorian, she stabs him in the groin with one of her knives. He pulls it out, and uses it to stab her in the chest. However, when she is seen lying on the bed, the knife has changed to Dorian's sword cane (easily identified by the different handle).
- Errors made by characters (possibly deliberate errors by the filmmakers): After the fight in the Dorian's library in which Mina has dispatched her victim in true vampiric manner, she opens and uses a compact mirror to aid in cleaning the blood from her face. However, vampires are not reflected in mirrors.
- Incorrectly regarded as goofs: When the League first sees Nemo's transportation, no one knows what to call it until Nemo tells them that it's an "automobile." Later, when the League is racing through Venice, Quatermain tells Sawyer to take the "car." If they had never seen or heard of an automobile, how would he know to call it a car? Actually, in British dialect "car" is used to mean any wheeled vehicle, and the word's usage pre-dates the invention of the automobile by centuries: c.1350 Middle English carra, from Anglo-French carre, from Latin carrum, orig. "two-wheeled Celtic war chariot," from Gaul. So it really is not surprising that Quatermain would refer to the vehicle as a car.
- Revealing mistakes: During the shootout in the African Club, we can clearly see Connery's stunt double.
- Revealing mistakes: When the Nautilus first arrives in the frozen wasteland, the heroes survey the scene from the conning tower. There is the sound of a biting wind and yet the snow is falling around them softly and vertically downward.
>>> WARNING: Here Be Spoilers <<<
Goofs below here contain information that may give away important plot points. You may not want to read any further if you've not already seen this title.
- Factual errors: SPOILER: During the fight between Sawyer and soldier armed with fire thrower, Skinner manages to damage the thrower's gas tank and is immediately engulfed in flames. However, Skinner is invisible, meaning he is naked and the human body is virtually flame retardant. It would be next to impossible to turn Skinner into a human torch with the gas flame thrower (the only way to set a man alight is to use some substance that sticks to the skin [like napalm] or has flammable vapors [like gasoline]).
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