Revealing mistake: The T-rex does not leave or make any footprints in the soft mud during the attack on the car.
Continuity mistake: When Nedry hears the Dilophosaurus and turns around, he's holding a tow cable. It's gone in the next shot.
Continuity mistake: The T-rex completely destroys the outdoor bathroom facility that the lawyer ran into. The lawyer is perched atop the toilet and the remaining damaged wall behind him is tilted backwards. When the camera cuts to a shot where the lawyer is seen from behind and the T-rex is just about to eat him, the wall is missing. When it cuts back to a front shot, the wall is back again.
Continuity mistake: When Grant shoots at the window in the control room, and we see the holes, they are holes from rifle bullets. But the shell casings on the floor is from a shotgun. And yes - shotgun shells do exist with one big slug in them, but then the holes in the glass would be a lot bigger.
Continuity mistake: When the T-rex is attacking the vehicle with the kids inside, Alan gets out of the other car. Even though it is pouring rain and Alan is standing perfectly still, no raindrops are seen hitting his solid, medium-colored shirt. It stays perfectly dry, even though there is nothing overhead that is shielding him from the rain. It is only after the scene cuts to him at the other car that the shirt is suddenly drenched. The rain is obviously CGI.
Continuity mistake: After Nedry has sprayed the shaving cream on his hands, (and after placing it on the pie) we see a sideview shot where he lowers his hands to his sides. The shot changes to the front and his hands are up again, drying his hands off with a napkin. It was too fast to move his hands.
Continuity mistake: When Ellie runs away from Muldoon towards the Power Station, she climbs over a tree and watches a path in front with two more fallen trees on the way. When she is about to jump over the first one some branches suddenly appear on the close-up to help her do the jump. Furthermore, when she is about jump over the second tree the close-up is a repetition of the previous tree.
Continuity mistake: In the scene from behind Dr. Grant we can see the cow being lifted straight up. You can see that the cow is rather close to Dr. Grant. Then the scene cuts and the cow is already in the middle of the top of the Velociraptor paddock. Judging from the distance between Dr. Grant and the paddock from the previous wide-shot, and the fact that Dr. Grant made no big moves, the crane couldn't pass that distance between the two shots.
Factual error: At the beginning of the film we are shown an amber mine in the Dominican Republic. This amber is only 45 million years old, Hammond would never bother buying the amber from there as dinosaurs disappeared from the fossil record 65 million years ago.
Continuity mistake: At the site of the T-Rex attack, Ellie and Muldoon help the injured Dr. Malcolm into the back of the Jeep, before Ellie goes looking for the other Explorer. Muldoon hears the T-Rex approaching and shouts "Ellie, come on!" but Ellie spots the Explorer over the wall and (in the next shot) she and Muldoon (heard but unseen except for his torch beam) have left Dr. Malcolm alone, somehow descended the high wall, and are running up to the wrecked Explorer. There is no implied time gap between the shots as they could hear the T-Rex was approaching before they did (or did not) descend the wall and later the T-Rex is almost at the Jeep (now in a different location) and Dr. Malcolm is urgently calling them back.
Continuity mistake: When the T-rex is attacking the kids in the car, in the shot where it stands on top of the car, the metal begins to buckle in the next shot inside the car. When it starts to sink, the metal isn't buckled and you can see the car sinking into the mud pit.