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 was meant to escape from the boat when it pulled in to the harbour, but they cut the scene from the film and now that bit doesn't appear to make any sense.] (01:40:55)
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. (01:38:10)
Suggested correction: Ludlow already established that it's nighttime, not morning, when he says "tonight we christen Jurassic Park San Diego." He says this will happen in 30 minutes, so he's not talking about "tonight" being 13+ hours away. The sentence you're referring to was just the beginning of a different part of his speech which was interrupted and the "wee small hours" wasn't referring to that moment. He could have been talking about all the early mornings they put in in the past, or they all showed up at various times that morning and waited around till that moment. But it wasn't morning and he never said it was.
Bishop73
Suggested correction: This is completely wrong. For one thing, the Raptors being on the cargo ship was NOT used in any way; just a photo that never went any further. Second, there's a storyboard showing exactly how the T-Rex got loose and you can actually see this in the film; meaning the damaged cage and the cargo hold looking as if the T-Rex was trying to escape. I highly recommend checking out Klayton Fioriti talk about both the deleted scene and scene in the film on YouTube for more information. Either way, it makes sense when you look into it.