Character 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. (00:32:30)
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.
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.
Suggested correction: While you are right, it's still not that much of a mistake because not only does it tie into the Butterfly Effect from the first movie, but also maybe Roland used it to his advantage, meaning an opportunity to shoot the Buck Rex since using its baby didn't work.
You're really grasping at straws on this one. The top priority for everyone at this point is to find safe shelter. A bunch of dinosaur experts aren't going to jeopardize that by allowing someone in their group to walk through dangerous territory with blood-soaked clothing, and Roland isn't going to risk the lives of other people to hunt the T-rex. This is just bad writing by the filmmakers, plain and simple.
What butterfly effect?
He's talking about when Ian Malcolm was explaining chaos theory and used the term "butterfly effect." But like Phaneron said, the person was really grasping as straws and this scene has nothing to do with what Malcom was talking about.
Suggested correction: I don't think this is actually a mistake. Yes Sarah's jacket is covered in blood from the baby T-Rex, but as you say they've got to pass through Velociraptor territory. In JP3 it was noted that the T-Rex pee keeps smaller dinosaurs away but actually attracts the Spinosaurus. The scent of the T-Rex blood could actually also have the same effect as the pee at keeping the smaller dinosaurs away.
Continuity mistake: When the T-rex is in San Diego and is about to smash the bus, the driver tells everyone to get to the side. There is a guy in a seat right behind the driver, but when we go outside the bus just before the T-rex crushes it, that guy is no longer there. (01:52:05)
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)
Suggested correction: The idea of raptors being on the boat is a myth (likely spawned from a similar thing happening in the first book's ending). Though it's very poorly communicated and leaves many unanswered questions (the captain's hand the least of which), the dead hand holding the cargo hold controls implies that the T-Rex somehow got free, killed the crew, then was either lured or willingly returned to the hold where a dying worker closed the doors again.
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. (01:55:20)
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.
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. (01:48:35)
Audio problem: The ship is going at full speed towards the coast - making a roaring engine sound. But when it hits the coast and stops, the sound of the engines stop too. Who turned them off? (01:46:25)
Visible crew/equipment: In the scene in the shed towards the end, when Sarah and Kelly are at the top, you can see the harnesses that are keeping them safe. (01:35:35)
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 animatronic dinosaur's 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. (00:46:40)
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. (00:11:40)
Factual error: When Roland is walking in the pouring rain and talking about killing the T-Rex, he has his gun slung over his shoulder vertically and barrel-upwards. If you were to do this in real-life in a tropical rainstorm for very long, you would run the risk of water entering the barrel and causing problems with the gun. And as a professional hunter Roland would know better. (01:07:50)
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. (01:46:52)
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. (01:30:10)
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. (00:26:20)
Continuity mistake: When the second INGEN team is rolling through the open field and you first see Rolland talking to Peter about not setting up camp on the game trail, if you look carefully in the shot looking at Peter they are actually on a paved road instead of open field. Split second mistake. (00:32:55)
Continuity mistake: In the scene where Sarah is hanging from the roof surrounded by 'raptors, the position of the roof tiles she's holding on to change between shots. (01:33:35)
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. (01:23:55)
Continuity mistake: At the San-Diego docks, the guy says it's the 'wee small hours of the morning', yet when he goes inside the Harbour Master's control room, the clock on the wall says 9:25. (01:38:20)