Revealing mistake: When the T-rex escapes into San Diego, it enters someone's backyard to drink from their pool. When the Rex plunges its face into the water, the water barely ripples and its bottom jaw is as clear as day below the surface of the water. If a beast of that size were to dip its head in the water, no matter how gently, it would've created a ripple that would distort the surface of the water quite significantly. (01:45:20)
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)
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)
Other mistake: Immediately after the T-Rex breaks out of the facility into San Diego there is a panning shot into a cabin room, which is filled with people, none of whom are showing any reaction to the T-Rex. (01:47:10)
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)
Factual error: After Ian and his girlfriend get the baby T-rex from holding in San Diego, they track down the big T-rex. They pull into a gas station and the Trex knocks the large 76 ball towards them. The problem with this is that that gas station/intersection is not in San Diego, CA but in Granada Hills, CA. The cross streets are Rinaldi and Balboa. (01:49:00)
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)
Visible crew/equipment: When Ian and Sarah (with the baby T-Rex) are pulling into the gas station, if you look in the rear view mirror, you can see the heads of a number of crew members watching. (01:53:47)
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)
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.
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.
Revealing mistake: When Kelly does her acrobatics and kicks the raptor out through the window it is possible to see that the raptor is pulled through the window as it "flies" upward and scrapes against the top of the window frame and then straight down. As the raptor falls down 2 wires can be seen reflecting light outside of the window, one even falls down after the raptor.
Factual error: When the T-Rex grabs Eddie out of the car, as soon as it takes its foot off the hood the car shoots forward and both it and the trailers fall off the cliff. In reality this wouldn't happen, the trailers would have simply started sliding again slowly. It's also shown that the cars wheels start turning faster as the car picks up speed going forward. Eddie had the car in reverse, as soon as his foot came off the pedal it would have stalled meaning the wheels wouldn't have turned and instead it would have just been dragged like it was doing before he got back behind the wheel.
Suggested correction: If during the time Eddie was being dragged out of the car the clutch was pushed into neutral (it's a manual), all the force the car applied to keep the trailers from falling would have disappeared and basically any way for it to go slowly as well.
Factual error: In the last scene of the movie it shows the adult Tyrannosaurs and the baby. Then it shows a Pterosaur. If you put on subtitles it says [Pterodactyl shrieking.]. Those couldn't be Pterodactyls, since Pterodactyls were much shorter and had no crest. Those Pterosaurs are in fact Pteranodons.
Continuity mistake: After Malcolm and his team are rescued at the edge of the cliff by the Hunter and his team, the "movable feast" begin their journey to the abandoned site. As the music plays and the trek commences you might notice that the footage shot in Hawaii has the Hunter's hat off. This is intercut with the footage shot in California with the Hunter's hat on. It can get distracting.
Factual error: When Hammond is talking with Malcom about going to Site B he says that the departure is from San Diego which is "a couple of hours" away from there. A flight from San Diego to Costa Rica would take over 5 1/2 hours. Then there is the trip to the island.
Deliberate mistake: When Sarah, Ian and Nick are climbing up the cliff with the rope, Sarah is able to easily pull the rope up to place her hand underneath it for a better grip. The rope is quite lax for having three full-grown adults hanging from it.
Continuity mistake: The cracks in the rear window of the lab truck when it's hanging over the side of the cliff seem to vary between the shots outside underneath vs shots inside as to where they are in the glass. There is a major one above (not underneath) Sarah's hand that's visible from inside and not from underneath.
Visible crew/equipment: In the scene in the shed towards the end, when Kelly does her gymnastics, you can see that it is a stunt double.