Plot hole: How did the men on the ship get killed? The bridge was intact and the T-Rex was still inside the cargo hold. [A raptor escapes from the boat when it pulls in to the harbour, but they cut the scene from the film and now that bit doesn't appear to make any sense.]
Plot hole: Near the end of the movie, Peter Ludlow (the snivelling nephew of John Hammond who wants to create Jurassic Park in San Diego) is addressing company stockholders as they wait for the cargo ship to arrive. He says something to the effect of: "I'd like to thank you all for being intrepid enough to show up in the wee small hours of the morning." Those last six words, and the color of the sky make it seem like it is four or five in the morning at the latest. For that early, San Diego is a busy town. The buses are running, business men are out, video rental stores are open (and with plenty of customers), and generally a lot of people are out to run away from the T-Rex. I have to imagine that the mass of people running in terror (even though it is early in the morning) were put in as an homage to old monster movies. Same thing could be said for the Japanese business men.