First off, the best way to begin this investigation is to explain exactly how the boat came to be where it ended up. At Isla Sorna, the male Rex was captured by being tranquilized by Roland Tembo. After InGen Harvest Base was radioed from the abandoned Worker’s Village by Nick Van Owen teams of helicopters were dispatched across Isla Sorna to search and gather the survivors. The helicopters managed to locate Peter Ludlow and with him Roland Tembo with his living trophy. Then, using a cargo helicopter, the Rex, while caged, was air-lifted onto the deck of the Venture 5888 ship waiting out in the Pacific Ocean very near to Isla Sorna. The animal would have then been caged on the deck of the Venture until its health started to decline and those overseeing the health of the animal inadvertently administered a stimulant that would wake it up altogether before reaching the InGen Marina Complex at the San Diego port.
Let’s examine the big thing here and that is that these helicopters would have transported any of the caged/caught animals to the waiting Venture once InGen had finished their harvest operations. This was a cornerstone point of Ludlow’s plan going in to raid Site B. The cargo ship then would travel to San Diego with the animals safe and secure in their respective cages. This is basically what InGen had planned to do with all the animals it captured. As fate would have it the only animal that Ludlow and his team would make away with is arguably one of the most popular dinosaurs ever. Examining further with the Bull Rex on board and likely around the time the boat reached the American coast the Buck’s heart stopped. This is the very setup that leads to the crew of the Venture getting eaten by the Male Rex.
Once the stimulant had been administered the Male Rex broke out from its restraints and there was utter chaos with the crew scattering to avoid being turned into a meal for it. While it is possible that some of the crew survived below deck, we’re left with more questions than answers regarding that fact. One thing we do know is that the helmsmen came out of the bridge and the Rex saw him at eye level and ripped his body free from his hand which was gripping the wheel. We don’t see any external damage due to the way the camera doesn’t give us a fully in-depth view of the boat, but rest assured the context is that the Rex ripped the helmsmen hand off while dragging him out of the cabin. While we don’t see the cabin was damaged, we do know this is implied to have happened. In fact it really doesn’t matter if we see the cabin itself as the result is clear either way, the adult male brought back attacked the helmsman while they were trying to steer the ship while also eliminating the rest of the crew where it could.
What happened presumably next is that a person who had been mortally wounded managed to open the cargo hold where the remaining trying lure the Rex into the hold. The mortally wounded crewman still above deck then closed the hold which the Rex tried to exit from but was otherwise unable to do so. The male Rex caused the top of the hold to be shut in an uneven pattern as it tried to escape. The ship, now mostly crew less thanks to what happened, plowed straight into the dock and stopped once it hit the solid ground of the marina complex. Everybody that was waiting for the ship to arrive would ultimately board and discover the grisly sight of dismembered and eaten crewman along with causing the unintentional release of the Bull Rex onto San Diego.
After the Rex escapes we move to Sarah and Malcolm talking to a man in an InGen uniform. Seemingly this man knows things about the ship and what happened with the Male Rex in particular. It’s possible he was one of the crew that hid below deck or at the very least checked the log on the ship and deduced that administering the stimulant was what caused all the chaos. Unfortunately this is never explored beyond the fact he is wearing an InGen worker uniform or if he just read the ship’s log to find out the information. Again though, this is an attempt to explain what had happened in the events leading up to the release of the animal without over burdening the audience in unnecessary details. 
For a moment if we consider he was a crew member that hid below deck then logically these same crewmen also were too afraid to come up to the deck to check on what had happened and that would be because the incident had happened only minutes earlier so they didn’t have time to react and stop the ship from plowing into the dock.
Notice the distance between the hand, Ludlow, and the door. There is also no stress to the door, or to the door from the other side. Many will call this a flub and think it is implication for something else being responsible when there is no tangible and credible evidence for it.
So while there is no stress marks or broken areas on the bridge from the Rex to attack the captain/helmsman many will spout that this is counter evidence as the T.rex not being the only occupant from Isla Sorna on the boat. In fact because of this many insist Velociraptors boarded the boat, set the Rex loose, killed the crew, and conveniently jumped ship just before they reached San Diego’s harbor. There’s a lot of problems with a Raptors on boat theory. From a common sense standpoint no Raptor would hop off into the mysterious and unfamiliar deep water. Especially if the likelihood of a predator existing to eat it would be one of the concerns. Simultaneously, let’s examine it from a story telling perspective. Such a big setup for a sequel such as this would have been teased or strongly implied in some way or another. It wasn’t, and all confirmations say it was the adult male Rex on the boat doing all of this. Unfortunately all it does is it means the scene could have used more detail to show why and how it was the Male Rex doing this and ergo wasn’t as cleanly devised in the production by the creative powers behind the film as they were all focused on the audience taking it nothing more than face value.
It has been stated in numerous interviews post-release of the second Jurassic Park film that both Steven Spielberg and David Koepp say that there was no other animal on the boat besides the Rex. When we add this to additional evidence of the present dialogue that says the same thing we can deduce the truth of the matter. While aspects of it can be viewed as a flub it is important for to not create story for something that is already explained in the film itself.
