Continuity mistake: When Jeff Goldblum is trapped in the car with the raptor outside, the raptor bumps into the window, cracking it. There's no hole in the centre of the crack in the shot of the raptor, but when we see a shot of Jeff Goldblum a second later, there's suddenly a hole in the window.
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.]
Other mistake: When they're on the island and the INGen helicopters are flying in, Jeff Goldblum takes the binoculars and looks through the wrong end.
Visible crew/equipment: When the T-Rex is running rampant in the streets, we see a guy running away from it. He tries to run into a video store, and the shot is from inside the video store. Right before that guy gets eaten by the Rex, he runs to the door to try to open it. And when this happens, you can see the reflection of the cameraman in the glass on the door walking towards it.
Character mistake: Sarah is a trained expert with predatory animals. But when her jacket is covered with blood (and not just any blood, the blood of the infant T-rex), and they're in a forest surrounded with carnivorous dinosaurs, and she knows that they need to pass through Velociraptor territory, and she thinks that the T-rex might follow them, she doesn't think to take the jacket off. And the others, who also happen to be hunters who would surely know that the blood would attract predators, don't say anything about it.
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.
Continuity mistake: When Sarah walks through the water when she sees Malcolm for the first time on the island her pants are soaked up to mid thigh, in the next scene she is running through the water again and her pants are only soaked up to her knees.
Visible crew/equipment: When Sarah and Nick return to the trailer with the baby T-rex, there is a shot of Nick carrying the rex towards the operating table. Look between the baby rex's legs - there are a series of wires leading from a opening in the anamatronic dinosaurs belly to a bulky device (presumably a battery pack) in the actor's pocket. Once you know where to look for the wires, you will notice them in many other shots in the film when various actors are holding the baby rex.
Visible crew/equipment: When Ian is talking to John in the bedroom you can see a mirror. After John tells him about the project, the camera moves to the bed and there is a reflection of blue jeans, probably the cameraman's.
Deliberate mistake: When the ship crashes into the dock, all of the scenes leading up to the crash and after it show a clear view across the harbor as we can see lights and land on the other side. It's not until the ship is about to crash that a thick and dense fog appears and disappears within a minute to mask the ship to create a more dramatic effect.
Continuity mistake: As the team are making their way through the long grass and are attacked by the Raptors we see a black man holding a torch turn around and look up into the air and scream. The camera changes and then the Raptor jumps in the air and on to him. He looked up into the air before there was anything in the air to look at.
Revealing mistake: When the stegosaurus begin to move around a lot, you can see the one that is charging at her steps in the creek water, but there is no splash or any ripples.
Continuity mistake: In the end part of the movie where Kelly, Sarah and Ian are lying on the couch and Sarah and Ian are asleep, you can see that Sarah doesn't have a blanket. However, when the shooting is back at the couch after the television shot, Sarah is now having the blanket. The blanket should have been seen in the first mentioned scene.
Continuity mistake: Near the end of the film, when Drs. Malcom and Harding are looking for the baby T. Rex in San Diego they arrive at the new InGen Jurassic Park. The car brakes hard, skids a little pulling a trailing cable for a portable light. The lamp falls. When they get back into the car with the baby T. Rex, to use it to entice the adult back to the ship, the lamp is standing again.
Continuity mistake: When they're in the shack, and the raptors are making the walls shake, the lights wire guard falls off the wall and lands in front of the door. We then see a closeup of the raptors starting to dig under the door, there's no sign of the light guard. We then cut back to a wider shot of the door, and the light wire guard falls off again. Eventually it shows a closeup of the light wire guard AGAIN falling off.
Revealing mistake: When Sarah is making her way to the baby Stego, just before she gets on her belly and crawls closer to it, you can see the kneepads she has on.
Continuity mistake: The day after the T-Rex attack, when they are all walking towards the control complex, Sarah is asked about the blood on her shirt, and answers that it's from last night, but it's too humid for the blood to dry. Nevertheless all their clothes - which ought to have been soaked during the rain storm, are completely dry.