Wooden chairs on deck vanish before the Nautilus submerges.
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.
When Nautilus appears for the first time, it is over 8 stories tall, to impress the audience. However, in Venezia, it is much smaller (about 2 stories tall) so that it can fit in the narrow and shallow canals which it could not have entered in the first place because that canal is obstructed by low bridges on both ends.
During the capture of Mr. Hyde, his clothing is shredded, indicating he started out dressed in his Jekyll form before the chase. His top hat, however, is Hyde-sized, as revealed when Sawyer picks it up.
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.
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".
In the Kenyan bar fight, Quatermain pushes one of the armoured 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 armoured vest should have blocked the passage of the horn.
When Quatermain and Sawyer are shooting off the Nautilus, the balls launched by the crewman are about a foot in diameter. The balls appear to land in water about 50 meters from the ship while Quatermain brags about shooting these at 500 meters or further. Had the balls been launched to 500 meters, they would have had to be much heavier to fly that far and would be barely visible as dots on the water, not as clearly and close as in the movie.
It is late July by the time the League arrive in Venice, where Carnival celebrations are underway. However, Carnival season ends in early spring, with the last day before the season of Lent begins. Even in an alternate universe, this would still apply.
Nemo introduces his invention as an "automobile." Later in Venice, Quatermain tells Sawyer to take the "car." The word "car" (from Latin "carrum" for chariot) has been used in English to mean any wheeled vehicle since at least 1350.
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.
It is clearly established that the movie is set in an "alternative universe" and its geography, technology, and history must therefore be as the filmmakers describe. Venice could have graveyards and roads extensive enough to allow a car to drive around. In addition, the inhabitants of Venice might have been celebrating the Carnivale in 1899. (In our reality, Carnivale was banned by Napoléon Bonaparte when he invaded Venice in 1797 and not reinstated until 1980.) The name Kenya could be used for an entire country in 1899. (In our reality before 1920, the country was called British East Africa, and Kenya was the name of a mountain.) The reality is more advanced than ours, with military uniforms tending to be more typical of the 1910s than the 1890s, and words like "sonar" and "solar power" being thrown about.
After the battle in Dorian's library, Mina looks in a small mirror to tidy herself. While many mythologies state that vampires cannot reflect in mirrors, no such rule is given in this film.
Allan Quatermain and Dorian Gray both jump from Captain Nemo's speeding car as they race through the streets of Venice, and land on their feet, even though the car was moving at a high rate of speed. In a superhero movie, some leeway is allowable for "toon physics," with Quatermain being on the Batman side of the superhero equation.
We should at NO POINT see Skinner's 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.
Skinner has to be nude to be completely invisible, but when the League are tramping through the snow toward shelter, his feet leave shoe prints.
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.
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.
When 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
When Mina is telling her origin story to the League, a radio earpiece (presumably to feed Peta Wilson her lines) is visible when her hair is pulled up in a high bun.
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.
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.
The radio message directing the League towards Mongolia is only long enough for 15 to 20 characters, not the multiple sentences in the dialog.
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.
When Skinner is transmitting his message to Nautilus he reports his heading as "east by northeast." There is no such compass heading. The direction should be either "east northeast," which equates to 067.5 degrees or "east by north," which equates to 078.75 degrees.
When the Invisible Man drinks from his glass of Scotch, the liquid can be clearly seen sliding down into his stomach, implying that all food and drink he consumes will still be visible inside his body. (This was a plot point in H.G. Wells' "The Invisible Man" and most film adaptations thereof.) Yet no such image recurs throughout the entire movie, suggesting he fasted the whole time, in which case he would be too weak for all the physical feats he performs.
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.
Dorian Gray's picture is much too big to fit in the space on the wall in his house.
In Venice Captain Nemo gives the command; "All ahead, Stop". This is actually two contradictory engine orders, which are impossible to execute at the same time. "All ahead" indicates that both engines should turn so as to give forward movement, but no engine power setting is specified. "Stop" indicates for both engines to stop turning. Further, we see the Nautilus's screws actually go into reverse, not stopping. They appear to be executing an "All back" order.
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.
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.
During the montage of the League members when Hyde is brought aboard the Nautilus, Dorian is shown to be plucking his eyebrows. This would be pointless since the immortality magic of the painting restores him in every detail, which means the plucked hairs would immediately grow back.