Revealing mistakes: When leaving the crystal spring, a long crystal bends when someone brushes against it, indicating that it's rubber.
Continuity: When Lindenbrook and Count Saknussem come back out of the sea after escaping the giant lizard, their footprints in the sand from running out during a previous take are clearly visible. It is not their footprints from running in.
Revealing mistakes: Near the end of the movie, when Alec is trapped in the tree at the convent, he falls and grabs one of the nearby sheep to disguise his nakedness, you can see the shorts he is wearing.
Audio/visual unsynchronized: Near the end of the film, when Hans is calling for his duck, Gertrude, his mouth movements don't match his words.
Anachronisms: Early in the movie, Oliver Lindenbrook speaks of the "stars and galaxies of outer space." In the 1880s, however, our Milky Way galaxy was believed to constitute the entire universe. Knowledge that other galaxies exist beyond our own did not come about till the 1920s. Thus a man of the 1880s would not use the word "galaxy" in its plural form.
Revealing mistakes: After bathing in the underground cavern, Alec places his hand on a rock to climb down after his lantern, and the rock moves as if it were made of plaster.
Revealing mistakes: When Alec attacks the lizard's tongue with the chisel, the point he hits is a different color to the rest of the tongue, making it obvious where the fake blood is set.
Continuity: The rope that Carla trips on while trying to escape the dinosaurs is shown to catch the tip of one of her boots, then around her ankle, then at the tip of her boot again.
Revealing mistakes: When Hans wakes up on the beach and is shouting for Gertrude, there is no echo. When the rest of the party is shouting for Hans, there is an echo.
Continuity: When 'Atlantis' is discovered, Mason is heard delivering one line in a regular voice and the next in a voice with an echo without changing locations.
Factual errors: There is no nobility in Iceland (in fact it is the oldest democracy in the world), therefore Count Saknussem, who seems to be an Icelander should not be a count.
Errors made by characters (possibly deliberate errors by the filmmakers): After the explorers are washed ashore, the Count eats Hans's duck, Gertude. When Hans approaches him with murderous intent, the Count addresses him in English, pleading for his life, despite allegedly being native Icelandic by birth and knowing by experience that Hans only understands Icelandic.
Crew or equipment visible: Camera shadow on Lindenbrook when he gives the university officials the plumb bob.
Revealing mistakes: When Goteborg gets in the carriage and leaves the volcano, tracks from the wheels are visible. The tracks end, as if the carriage had backed into its position.
Errors in geography: When Lindenbrook is in the carriage after being 'kidnapped' the topography appears to be more appropriate to the American desert southwest than to an island located at the Artic Circle.