Plot hole: When they find captain Nemo's journal the journal is completely intact and the pages are made of paper. But the journal is very old, and the island sinks every 70 years, so the journal should not have looked that good, and the pages must be gone by now or at least not that readable. (00:47:30)
Plot hole: As the island is sinking you can see parts break off, like the island is falling apart, but if it does this every 70 years then there wouldn't be an island. It should have completely fallen apart hundreds of years ago.
Other mistake: Big animals are small and small animals are big on the island, but Alexander has fireflies in a jar at his treehouse. If animal sizes are reversed on the island, the fire flies should be very large, similar to the bees that show up later in the movie.
Character mistake: When Sean and Hank are trying to get to the Nautilus, they swim right through a big school of jellyfish. Seems really unlikely that Sean, raised by a scientist and Hank, an ex Navy man would do this, considering how many species of jellyfish can give a sting ranging from agonizing to deadly. And, while they have a limited oxygen supply in this scene, and time is a factor, the scene shows there is room to swim under them. They actually pause in the middle of the school to grin at each other. There would have been sufficient time and oxygen to avoid the school.
Answer: There is a deleted scene on the DVD/Bluray where they attempt to give an explanation. Kailani asks "What happens to the animals when the island sinks? They can't all die!". Alexander replies "Even the mammals develop quasi-amphibian characteristics. They just burrow below the ground's surface and absorb the oxygen through their skin."
Sierra1 ★