If the worm-creatures are all part of one creature, why do they thrash around and fight each other for meals on occasion? Cephalopods have several "brains" across their main body and each tentacle. The limbs are mostly on auto-pilot.
Why do the worms smash their way through doors before the galley scene and then start closing and even locking them to herd the characters afterwards? The tentacle that sneaks up behind Mulligan has to have come through the hatch Finnegan closed and locked, which means that the monster just figured out how to open the door locks, and is immediately putting that knowledge to use.
During the climax, why does the creature hold Finnegan up to its eye rather than just swallow him with one of its tentacles? If it's anything like a normal cephalopod, then it's fairly intelligent and likely curious. Remember, the tentacles catch prey with touch and sound, so the creature probably wants to actually see the little things that have been causing it so much trouble.
Those fairly likeable characters like Leila who died? They all died a slow, agonizing death.
The text that appears on-screen at the very beginning says that the cause of all the South China Sea ship disappearances has never been revealed. It doesn't say "until now" or anything like it, which rather implies Finnegan, Joey and Trillian won't be getting off that island alive to tell their story.
Why would anything that feeds on the body fluids of its prey have so many teeth? Biting into flesh with them would spill the very fluids being sought.
We see whale skeletons at the end, so presumably it has drained whales as its prey. The various fangs could be used to fight and kill such creatures, or to help hold onto larger prey while trying to devour it.
Why did Trillian even try to rob the vault so early in the cruise ship's voyage? She didn't know anything about the plot to sabotage the vessel, let alone the monsters, so for all she knew she'd be stuck on board for days, hiding whatever she'd stolen as the ship was searched.