Revealing mistake: When the T-Rex has a raptor in its mouth at the end, the raptor disappears completely from the T-Rex's mouth for one frame. It's just after it's picked up - the T-Rex swings it left, then right, and as it swings to its left again the raptor disappears. If you want to be even more precise, there's a slatted/stepped white bit above the door - the raptor disappears about 3 frames after its foot moves above that white bit. (01:52:20)
Revealing mistake: After the T. Rex has flipped the Explorer upside down there's a closeup of Ian, and when it cuts to the T. Rex chomping away on the tire while the Explorer moves around, we can see that the acrylic glass roof is attached to the vehicle with thin cable wire - holes were drilled in the acrylic glass roof and sides of the vehicle.
Visible crew/equipment: After Alan, Ellie, Lex and Tim run into the control room Alan tells Ellie to boot up the door locks, and when the Raptor opens the door Alan drops his gun and we can see two distinct reflections on the glass - the Raptor's puppet head on someone's arm as it pushes on the door from outside the room, and also the reflection of a crew member (presumably standing in the camera area).
Continuity mistake: When both Explorer vehicles are parked at the paddock, in the shot of the goat being raised to lure the T. Rex, the "No! Feeding..." sign is permanently affixed to the front of the concrete wall, but in the previous and following shots that same sign is affixed to the angled top part of the wall. Later, when the power goes out, that sign is once again affixed to the front of the concrete wall.
Other mistake: When Dr Grant and the children reach the perimeter fence, Dr Grant tries to see if he can fit through, to no avail. When he and the kids start to climb, however, it is quite obvious that both Tim and Lex would have been able to crawl through quite easily, and that only Dr Grant should have had to climb over. Partly this links to the mistake here, where the holes in the fence are much bigger in the first shot, then when he tries to widen them he's holding a different part of the fence where they're smaller.
Revealing mistake: When Nedry is attacked by the Dilophosaurus, (the spitting dinosaur), the first spit supposedly lands on his shirt, BUT if you look closely, Nedry slaps it there himself with his hand - there's only a little bit on his shirt before he hits himself, then there's loads. (01:10:40)
Continuity mistake: At the badlands, when Hammond's chopper has landed and Grant goes to the trailer to open the door, if you watch the hinges of the door, they're on one side then it cuts to the inside of the trailer and the hinges are on the other side. (00:09:45)
Continuity mistake: While Lex and Tim are hiding in the kitchen, just as the Velociraptors come in Lex tells Tim to follow her, and when they turn into the aisle there's a stainless prep unit with no open shelves right beside them at the end of that aisle, but after the closeups of the Raptor's claws, when the kids continue to crawl away that prep unit has oddly vanished - the last unit in that aisle has shelves, and then it reappears when Tim sits under the utensils.
Visible crew/equipment: While Alan and Ellie are trying to keep the Velociraptor out of the control room Lex is on the computer trying to find the file to restart the security systems, and after Tim shouts, "Come on Lex!" it cuts to a closeup of the Raptor's claws at the door and we can see the crew member's head.
Visible crew/equipment: After the T. Rex flips Explorer 4 upside down it continues to attack the vehicle with the kids inside, and when it cuts to the T. Rex chomping on the tire, as the vehicle moves around we can see the hanging bundle of wires leading up through the window and also what looks like a crew member or something else that shouldn't be there, outside the vehicle behind Lex. Even if the wires were to belong to the Explorer they shouldn't be leading up and outside the way they are.
Continuity mistake: When the baby dinosaur is born, one minute the robotic hand is there behind the egg as it's hatching, then in the reverse angle the hand's suddenly disappeared. (00:27:30)
Visible crew/equipment: When the T-Rex is knocking the car with Lex and Tim in it, he knocks it once, and then again making the Explorer flip over. If you watch carefully, you can see a big wooden pot containing one of the fake trees for the set and a stage light. This mistake has since been corrected on blu-ray. (01:03:40)
Continuity mistake: After Ellie injures her foot running from the raptor, her limp switches legs repeatedly for the rest of the film. (01:40:10)
Continuity mistake: When the helicopter first lands on the island it is clearly not on the cross on the landing pad. Later in the scene it is. (00:17:25)
Revealing mistake: During the scene where Dr. Grant and the children are forced to climb a fence to flee from an unseen dino, there's a brief side view of the fence that clearly shows that it isn't continuous - it is probably only about 75 feet wide. (01:36:35)
Continuity mistake: When Grant grabs onto the electric fence, his hands are a short distance apart and there is a set of vertically positioned wiring in between his hands - the warning sign is also barely covering the "hole" in the wires. A couple of shots later, without letting go of the fence, his hands are much further apart and there are now three sets of vertically positioned wiring in between his hands. The angle of the wires also changes, and the sign is now well into the "hole", very near his hand.
Continuity mistake: In the scene with the T. Rex breaking through the glass roof, as the glass breaks one of the rex's front teeth breaks off and flies backward. On the next close-up of the dinosaur's mouth, the tooth is still missing, yet it is back in all shots after that.