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(at around 1h 3 mins) When they arrive at the T. rex cage right before the black out, we can clearly see the ground inside the cage is approximately flush with that outside the cage. But when the T. rex escapes and begins to terrorize the two trucks, the ground in the cage is shown to be at least 100 feet below where it was before.
Hammond has a pronounced Scottish accent at the start of the film, which deteriorates markedly in just a couple of scenes. By the end of the film he has an upper class English accent.
(at around 1h 3 mins) Gennaro runs off and leaves Lex and Tim in the Explorer when the T. rex appears, and leaves the car door open. Later, we see the same vehicle through the windscreen of Grant and Malcolm's vehicle and the same door is closed. Later on still, Tim shuts the door which is what attracts the T. rex' attention.
(at around 25 mins) The mosquito that is encased in amber, and from which the DNA sample is extracted is male. This is evident from the "bushy" look of the antennae. Female mosquitoes have far fewer hairs on their antennae, and so the distinction is easily made. Only females drink blood, as it is needed to produce eggs. There would not have been any dinosaur DNA in the male to extract. To make it worse, in that species of mosquito, Toxirhynchites, both the males and females are flower feeders, and would therefore have no blood, or dinosaur DNA in their stomachs.
(at around 1h 40 mins) When Tim is electrocuted, this would not really happen. Before climbing, you see the horizontal cables are held together with vertical cables so all fence wires are live AC voltage. The fence(like those to contain cattle\sheep etc) works when the dinosaur touches the fence and ground at the same time completing the circuit. That's how birds can sit on live power lines.
Dominican amber is famous for its quality, but it was only formed 20 million years ago, long after the dinosaurs had died out, so you could never find a prehistoric mosquito that had fed on dinosaur blood there, and even then, one that was completely uncontaminated, which would have been amplified along with the DNA, as well as too degraded. There is nothing to compare it with.
Incorrectly regarded as goofs
(at around 5 mins) Dr. Grant is shown at the beginning of the film excavating a velociraptor in Montana. True velociraptors have only been found in central Asia, but Montana was home to the closely related Deinonychus, which some paleontologists considered to be the same as Velociraptor at the time the original Jurassic Park novel was written. For the movie, they kept the incorrect name.
Many of the animals are depicted inaccurately, but this can be explained within the storyline - the InGen scientists have made mistakes or deliberate alterations to the species they cloned. They combined Velociraptor with Deinonychus, made Dilophosaurus a dwarf, and gave Brachiosaurus a chewing ability.
If Site B was where the dinosaurs were bred (In The Lost World: Jurassic Park (1997)) then why was the velociraptor born on Isla Nublar? Hammond wanted to create the illusion that all of the animals were, in fact, created on Isla Nublar. It isn't until The Lost World that it was revealed that Site B on Isla Sorna was where the large industrial compound producing thousands of embryos for a single viable one was located. This is explained in the novel but not mentioned in any of the movies.
(at around 1h 24 mins) When Grant and the children are sitting in the tree overlooking the Brachiosaurs, and again when climbing the electric fence (at around 1h 40 mins), the soles of Grant's boots can be seen and are completely clean and free of any mud or debris.
(at around 54 mins) "Surveillance camera" views displayed on computer monitors are obviously video clips that are being played back from disk (progress meter on the bottom).
(at around 1h 40 mins) In the climbing of the electric fence scene, there is a shot where it is plainly seen that this is a mere section of fence, and the actors could easily walk around it.
(at around 1h 50 mins) After the kids escape the kitchen they're in the control room with Alan and Ellie. Lex is getting things running on the computer while Alan and Ellie are trying to hold the door closed to keep the velociraptor out. Ellie tries to get the gun with her foot but cannot get hold of it. Since Tim wasn't doing anything there was no reason he couldn't have gotten the gun for her.
When they take the tour in Jeeps, they stop at the T-Rex spot. The T-Rex is a no-show to eat the goat. They move on and see a Triceratops and go back, only for the power to go out back in front of the T-Rex and goat.
(at around 5 mins) At the dig site where the lawyer shows up (only to find that Grant is not there), they call the manager to a find. The manager tells people to aim their light on the find. Looking at the directions the people are aiming their lights, only one light hits the mosquito in amber.
(at around 1h 6 mins) When the T. rex is attacking the car with Lex and Tim, in a shot through the roof wind-shield, you can hear them scream. However, their mouths stay closed.
(at around 1h 55 mins) When Lex falls through the ceiling, she is screaming but her mouth isn't moving.
(at around 45 mins) When the goat is offered to the T. rex, you hear the bleating sound of a sheep as opposed to a goat's bleating sound.
Crew or equipment visible
(at around 32 mins) When the raptors are being fed for the viewing of the visitors, a crew member's white shirt can clearly be seen shaking the leaves in the pit as the raptors attack their prey.
(at around 1h 45 mins) Arm of crew member when the velociraptor first enters the kitchen. The velociraptor was actually a full, but generally immobile, robot.
(at around 1h 6 mins) A studio light and a potted tree are briefly visible in the background when the T. rex flips over Lex and Timmy's car, as well as a number of cables and wires attached to the car. These have been digitally erased in the movie's 3D re-release in cinemas and on Blu-Ray.
Errors in geography
(at around 13 mins) Nedry is shown seated at a beachfront cafe behind the caption "San Jose, Costa Rica". San Jose is a landlocked cosmopolitan capital of almost 1 million people, situated 50 miles from either coast, without any adjoining lakes.
(at around 40 mins) The tropical storm is reportedly some distance west of the island. At the latitude of Costa Rica, tropical storms move east to west. The storm should have moved away from the island.
(at around 1h 20 mins) Just after Malcolm is rescued, you see him sitting in the back of the jeep in the T. rex area next to the other vehicle viewing the tremors in the water. In the next shot he is hurrying the others to come to the vehicle and they are in a completely different area of the park.
When the T. rex first gets out, it claws open the fence and walks through the opening; however, when Dr. Grant and Lex go through the same spot in the fence, there is a significant drop (large enough for a jeep to drop past them and into a tree that Dr. Grant then climbs to rescue Tim). The dropoff that Dr. Grant and the kids scale down would have made the fence too tall for the T. rex to reach or even see.
(at around 20 mins) The plot centers around finding dinosaur blood in fossilized mosquitoes trapped in amber. However, our first encounter with extinct life comes when Ellie examines a leaf and says "This 'veriforman' species has been extinct since the Cretaceous." No mechanism is provided for how they could have cloned the plants, given that mosquitoes don't drink plant juices. It is possible that DNA could have been extracted from the amber (hardened tree-sap), but this still doesn't account for other types of plants, such as ferns and bushes.
When Dr. Grant and entourage arrive on the island, the place is crawling with people: dock workers, game keepers, gardeners, kitchen staff, lab scientists, veterinarians, engineers, maintenance workers, builders, etc. A short while later virtually everyone has left for the mainland save for 4 people in the control room. And all of that because of a simple tropical storm common in these parts? Implausible and improbable.
(at around 57 mins) In the embryo freezing chamber, Tyrannosaurus rex is spelled with only one "N" instead of two. Also, Stegosaurus is spelled "Stegasaurus".
(at around 46 mins) Grant says; "T-Rex doesn't want to be fed. He wants to hunt. Can't just suppress 65 million years of gut instinct". However he has it the wrong way round; dinosaurs had 200 millions years of gut instinct; 65 million is the period for which they were extinct.
(at around 42 mins) In the scripted audio tour, the narrator refers to the dilophosaurus as poisonous, when in fact if the method of toxin exchange is spitting or biting, then it is actually venomous.