How else could the T-Rex have managed to kill everyone aboard the ship, even the ones in places that were too small and confined for it to make it inside? Obviously it was another byproduct of the frog DNA mutation, like breeding in the first film. It basically Yoshi'd the crew to death. Or worse, what they got was Hypnotoad DNA, and the T-Rex mindfucked everyone to kill themselves.
T-Rex clearly could not have killed people on the bridge and other spaces that were too confined for him. However, if Raptors made it onto the ship, they could have easily disposed of the crew before making a suicidal attack on the T-Rex.
- This is shown in one of the deleted scenes to have been the case, however they escaped after killing the crew instead of taking on the T. Rex.
- Concept art for the film clearly showed extensive damage to the ship that was also present on set, but hard to see in the final cut. Details like the Buck's cage being smashed open from the inside, crushed pieces of the ship, and the side wall of the bridge being smashed open from the Tyrannosaurus ramming its head through it all support the notion the Buck alone was the cause of death.
Clearly, John Hammond wasn't the only one against the dinosaurs on Site-B being exploited. It wouldn't be a stretch to assume that there was a group or group members that would use extreme measures. It would explain how the crew got killed and how their remains ended up all over the place. The killer (possibly the one who explained to Malcom and Sarah what happened) was a crew member who waited until they were near San Diego and then did his thing, staged the scene, rigged the ship, then escaped in the chaos. The aftermath brings both public attention to InGen's actions and leads to the isolation of Site-B.
Clearly, Peter Ludlow wasn't the only member of InGen with a hard-on for exploiting the dinosaurs of Site B. It wouldn't be a stretch to assume that at least one of his Corrupt Corporate Executive board members thought they might be able to spin public support against Hammond and the dinosaurs through extreme measures. It would explain how the crew got killed and why their remains ended up all over the place — of course an InGen agent would want the public to think the dinosaurs were responsible. The killer (possibly one of the few surviving mercenaries, a "backup plan" as Nick Van Owen was Hammond's backup plan) waits until they're back at the mainland to make his move, kidnaps Van Owen (explaining his mysterious disappearance), staged the scene, rigged the ship, then escaped in the chaos. The mastermind likely intended the Rex to be heroically brought down by InGen agents, bringing them public support for a second invasion of Site B.
After infamously disappearing in this movie (save for one shot on a computer screen), the fate of this species was left up in the air. But recall how they no-showed the tour in the first movie. What if in addition to blinding spit, they also have the chameleon ability the Indominous Rex has later on — they're just more cavalier about using it?