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)
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.