For starters there's the other four castaways reverence of Cyrus Harding and how much of a priority they put in finding him during their arrival on the island; the narration itself notes that if there was a sudden calamity the other four would be too distracted to notice.
Then there's Pencroft and Herbert's relationship. The story tries to paint Pencroft as a Parental Substitute to Herbert, but since Herbert is a grown man Pencroft's affection for Herbert comes off as romantic.
Isaac Asimov notes in his afterward for the book that it's odd how when the castaways build their paradise and discuss how they have everything they could ever want, no one mentions that it would nice to have some women on the island.
Tabor island (AKA Maria-Theresa reef) where Ayrton was marooned, and which was long believed to sit at the stated location, was later proven to not exist at all. What's interesting is that the Ernest Legouve reef, a similar phantom island close to the purported Tabor's position, sits roughly in the same location as Verne's Lincoln island.
According to Cyrus, the Pacific Ocean will one day be replaced by a vast coral reef the size of a continent.
Tear Jerker: Poor Jup. Nemo's back story is probably also a qualifier. And the destruction of the colony after all the work they put into it is pretty depressing too.
Values Dissonance: While Fair for Its Day, it's still a bit of a shock when the narration cheerfully informs that Pencroff and Nab are naturally on kitchen duty since one's a sailor and the other a negro.
Neb in general is awkward to read now. While one gets the feeling Verne was trying to do right by Neb by pointing out what a perfect and wonderful human being he is, Neb's lavish devotion to his former master (whom he still refers to as Master without anyone correcting him) and the way the other guys leave him out of things for no reason is weird. The worst of it is when they train Jup and Pencroft says they won't have to rely on Neb as a servant now, like that's a given.