I don't think the Lost World boat scene was a plot hole at all. It was always heavily implied that raptors were behind the attack. There was no way the T-Rex could have done what happened, and besides, he was still in the cargo hold. The film is unclear about what happened to the raptors. Maybe they jumped overboard, maybe they got into the cargo hold and the rex took them out, maybe they were even killed in the crash. Either way, they obviously weren't on the ship anymore so the T-Rex became the immediate threat. Perhaps dialogue about the raptors was cut, or perhaps it was always meant to be a little vague and mysterious, but it was certainly implied that they were there. (The implication was especially clear to people in the audience who had read the books, where a raptors-on-a-boat scene did take place)
I recently rewatched the trilogy too. I still love the films just as much as I always did, but something did stick out at me this time and it kind of left a sour taste in my mouth. The trilogy - especially the second and third films - always treat the dinosaurs as movie monsters instead of animals. What I mean is, each film has the requisite "ooh and ahh" scene where the characters are wowed by the fact that there are dinos walking around, but after that the films seem to go out of the way to show that every dinosaur these people come across is going to try to kill them. Even when they come across the dinosaur equivalents of elephants, ostriches or giraffes, the dinos will try to kill them. Sometimes it makes sense - the gallimimus stampede from the first film I get. But other times, it really doesn't. Why would a huge flock of fish eating pteranodons feel the need to attack a group of humans? Why would a newly-released triceratops stick around to rampage through a human camp instead of just running into the woods? Why would a giant spinosaur with an island full of food take the time to casually stalk a group of barely snack-sized people? Why would a group of tiny scavenger compys attack a healthy full-grown man carrying a machine gun for no good reason? I get the monster movie feel and the excitement of these scenes, but I preferred the first film's slightly more nuanced approach where the dinos acted, for the most part, more realistically. I hope the longer play time of a videogame will allow Telltale to include a larger variety of interactions with dinos, instead of just "this thing wants to kill you" all the time.