Plot hole: They all drop their backpacks and bags 3/4 mile down into the hole before climbing by rope into the caverns to begin their journey. Later in the movie, they are all sitting deep in the caverns complaining about the lack of water supply. Suddenly the long-haired guy pulls out a large glass bottle of gin, completely intact and they all drink from it. There is no way his pack could have fallen 3/4 mile onto a hard surface without that bottle breaking.
Revealing mistake: When evacuating the flood through the broken stalactite hole, Madam and Mason are standing on some sort of platform to get through the hole.
Continuity mistake: After the professor makes his speech at the end, he is talking to Carla. He puts his hand to his chin then puts it down. It cuts and his hand is up again.
Revealing mistake: When the group is rescued in the Mediterranean, you can see waves smacking against the matte background.
Continuity mistake: When Professor Lindenbrook is on the ladder in his study there appears to be a mirror reflecting a fire above the fire place. When the rectors come in there is a picture above the fireplace.
Continuity mistake: At the explosion in the lab, Jenny is blown on top of a desk with straight lines down the side. Nowhere prior or after shots is there any such desk. The next shot, Alec is picking her up from the floor.
Continuity mistake: When they are in the sunken city, the haversack is put down on a rock with a hammer on top of it. In a later scene, the hammer handle is pointing in a different direction.
Continuity mistake: When they are climbing up out of the hole to avoid the rising water in the cave, as they show the hole from below the water is about two feet below the hole, however when shown from the top the water looks to be about six inches below the hole, this keeps shifting back and forth during that scene.
Revealing mistake: When the four travelers are riding up the volcano in the asbestos basin, they are obviously dummies.
Factual error: There is an explosion in the laboratory supposedly because the professor's assistant added too much aqua regia. Aqua regia will do a lot of things, but in an open furnace it will not explode.
Continuity mistake: Before the explosion in the lab, James Mason has his gloves, after the explosion he has to crawl around the desk only to find his gloves laying on the floor. Extra set?
Continuity mistake: When madam breaks the stalactite during the flood, there is a small hole which grows wider and smoother as the team evacuates.
Other mistake: The Count and the Professor jump into the water to save themselves from the dinosaurs (which can't swim). In the long shots, it appears they are out very far, in at least six foot deep water, but close up, the water they are in couldn't be higher than four feet. What's to keep the dinosaurs from grabbing the two if they're in water that wouldn' come up to the dinosaurs' kneecaps?
Audio problem: Throughout the movie when they are underground, when someone speaks sometimes you hear an echo and sometimes you don't.
Factual error: Iceland has had no titles of nobility for nearly 1000 years, therefore Saknussem can't be a "count".
Other mistake: While they're waiting for sunrise on the volcano the professor is carrying a rifle. Later on underground it's never seen.