This has probably already been mentioned, but the name of the ship in the movie was a huge bit of fridge brilliance for me. In the original novel, the ship used to sail to Treasure Island is called "Hispaniola". In Treasure Planet, it is called "R.L.S. Legacy". What are the initials of the original author of Treasure Island?
There's also the fact that, given the setting (Treasure Island... IN SPACE!), the story's been changed enough that the ship isn't really the Hispaniola anymore... but's it's carrying on the Hispaniola's Legacy.
Notice when Jim is next to his mom, he has a case of Teens Are Short. When he comes back, Jim is slightly taller than her now. Why? In a literal sense, Jim had a growth spurt, but in a figurative sense, Jim finally grew up.
Why does "cannonball", as in the diving term B.E.N. references, exist in a world where cannons shoot "laserballs"?
Maybe there are several different kinds of cannonball, and laserball is just one of those types.
They probably have conventional ammo as well as energy-based ammo in this universe.
Possibly a leftover from when cannon balls of some sort were actually used, sort of like in real life. No one uses cannon balls anymore, but the term is still with us.
What, exactly, was the nature of Captain Amelia's injury? She clutches her side like she broke a rib but doesn't appear to have trouble breathing; at the same time her arm is in a sling but she doesn't seem to have any problem using it; she must have hit her head extremely hard at some point (probably either when the boat flipped or when the mast was struck and the boom snapped across the deck) because she's disoriented and woozy... holy shit, Amelia, what the hell happened to you?! And why does none of it make sense?!
She's supposed to be bleeding but that was cut so I think she had something like shrapnel in her side, probably missed her lung or she might have just been pretending to be fine, especially when the pirates turned up and for her arm, she might have damaged the nerves in her elbow or something so she can hardly move her arm. I once ran into a wall and had to keep my arm in the position of having it in a sling because straightening it out hurt too much. After a while it was fine, like how Amelia's arm was later on in the climax.
She could bruised her ribs and arm. I once slammed my thumb and finger into my bedpost and it felt like I'd chopped them off. My thumb was sore for a few months after that, so it could be that she just couldn't move her arm without feeling intense pain.
More like Fridge Sadness but, Flint's selfish greed brought about the end of what was no doubt one of the greatest archeological finds in history. First he twisted and perverted Treasure Planet, then planned to destroy everything, simply to prevent anyone from taking possession of his gold. Even after his death, when he'd no longer need the money anyway! In the end, what happened to the planet is a criminal waste.