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 the Fantom breaks into the Bank of England, the soldiers inside are wearing Brodie (Doughboy) helmets that were not introduced until 1915. Given this is an alternative universe and the Fantom's men are using a 'tank' (also not introduced until 1915 by the British, not the Germans) this could be acceptable for that universe.
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.
Tom Sawyer says that he is from the "American Secret Service". However, the correct name of the agency is the "United States Secret Service", not the "American Secret Service" and this is not a mistake many agents would make (especially since the acronym for "American secret service" would be "ASS", and no self respecting secret agent would admit that he is an agent of "ass").
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.
After the Nautilus is repaired from "M's" bombs, Quatermain congratulates everyone on the job well done. Though he is the nominal lead of the 'league', it should have been Capt. Nemo as the Captain of the Nautilus who thanked everyone.
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.
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.
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.
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.
In Kenya, the last assassin to be shot by Quatermain 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.
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.
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.
When Quatermain leaves the building containing League headquarters and gets in Nemo's automobile, his coat has a storm cape. When he gets out of the car at Grey's, the cape is gone and does not reappear.
When Quatermain and Sawyer are practice shooting off the deck of the ship, the lack of wind or relative movement of surroundings implies the ship is motionless as they do so. However, when the camera cuts to one of the targets as it lands in the water, the ship is shown to be moving quickly.
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 Nautilus first appears rising out of the quay, the sheer size of the vessel should have displaced millions of tons of water, but the water level never changes. Add to this the fact that an inland quay would not be deep enough for a vessel with a draft like that of the Nautilus to submerge, nor to support/float a vessel of that depth were it to surface.
When Skinner drinks from his glass of Scotch, the liquid can be clearly seen sliding down into his stomach, implying that all substances that aren't part of his organism will still be visible inside his body. Thus, any food he consumes as well as the resulting feces should be visible at all times; however, Skinner appears to be completely invisible throughout the entire movie. This means his system must have been completely devoid of any consumed goods during his screen time, which is impossible given the amount of time food normally stays inside the human body (up to 18 hours) and the relatively short amount of time that passes between shots of Skinner. A grown man requires reasonable rations of food as well as liquid to power his body, especially someone like Skinner who burns additional calories keeping his often nude body warm at all times.
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.
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.
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.
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. 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 reality, the Carnivale was banned by Napoléon Bonaparte when he invaded Venice in 1797 and not reinstated until 1980.)
After the fight in 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. Vampires are not reflected in mirrors, however she could be looking at her teammates behind her.
On the grave marker of Quatermain's son, the name is spelled "Quartermain". Though the former is the official spelling, the latter is acceptable. Even the original author Sir H. Rider Haggard used the latter spelling on occasion.
Around 04:38, the Fantom fires a rocket at a Zeppelin airship. The rocket has an unnecessary cable attached, as if a grappling hook, then it vanishes after the Zeppelin explodes and the Fantom walks away. However, with the altered time line, Fantom could have been using an early model of a wire-guided missile and therefore giving commands through the cable to the missile already in flight. When the missile exploded the zeppelin, the wire dropped away.
When Quartermain is in the club in Africa and is toasting the Queen, The period this was set in was before the 2nd world war and before Queen Elizabeth's coronation on the 2nd of June 1953. However, the movie is set in 1899, during the reign of Queen Victoria.
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.
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.
In Dorian Grays home the outline of a painting is seen on the wall and its supposed to be the spot where his magic aging self portrait hanged until recently and looking at the spot the painting appears to have been there for a very long time, however he himself later reveals that if he where to look at the painting it would undo its spell and the accumulated aging would reverse back to him just as it happens later on. If looking at the painting was so dangerous why would it be hanging on the wall in his home where he could accidentally look at it at any time. Being portrayed as a very intelligent person his actions does not display it.
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.
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.
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.
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 Sawyer's 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.
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.
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.
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.
When the Nautilus is racing towards Venice, the framing shots show the submarine traveling at a great speed. However, when the scene changes to the characters on deck, there is no wind or any indication the ship is moving at all.
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, was Hyde-sized, as revealed when Sawyer picks it up.
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.
The goof items below may give away important plot points.
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).
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.
In Kenya, one of the assassins throws knives at Quatermain catching him to the wall on his shirt collar. He rips his shirt collar when getting out of it. When the last assassin to be shot by Quatermain is dragged back into town and commits suicide, their is no rip in the shirt collar.
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]).
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.
In the fight scene in Dorian's library, Dorian is shot at close range multiple times. Though his shirt appears torn to shreds, moments later his clothing appears intact as Mina is taken hostage and subsequently kills her captor. However, given that Skinner has reapplied his makeup (showing a certain passage of time) and Dorian is returning from the upper level (despite being shot at on the lower level), it is quite conceivable that he has changed his clothing.