At the beginning of the movie there is a scene where Malcolm tells Ludlow about the three deaths during the Isla Nublar Incident, however, there were five. Muldoon and the Gate keeper were killed by The Big One. Donald Gennaro was devoured by the adult Tyrannosaurus rex. Ray Arnold was killed by the Velociraptors, and Dennis Nedry is blinded and then killed by the Dilophosaurus. Ian probably didn't know that Dennis was killed, though and Hammond most likely never told the group about the Gate keeper since the group would not approve of the park if they learned a crew member was killed while moving the raptor before they see the park. They were also not mentioned in the Boardroom deleted scene, in which Muldoon, Arnold, and Gennaro are. A possible reason for this is that Nedry's death may have already been written off due to his sabotage of the park, and the Gate keeper's law suit was mentioned in the beginning of Jurassic Park so it may have already been settled.
The boat that drops off Malcolm and the team has a north korean flag on it and not a Costa Rica flag.. you can see a red star inside a white circle on the flag. the Costa Rica flag and the north korean flag look the same but the Costa Rica flag does not have the red star inside a white circle but the blue and white and red strips are the same.
When they're on the island and the InGen helicopters are flying in, Ian Malcom takes the binoculars and looks in through the wrong end.
When Nick Van Owen takes the baby T. rex, you can see a bottle of scotch and a mug that wasn't there the first time we see it. This inconsistency can be explained by a deleted scene were Ludlow stumbles into the area in a drunken stupor to converse with Roland, only to fall and break the baby T. rexes' leg.
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 is a series of wires leading from an opening in the animatronic dinosaurs 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.
There is no proper explanation as to how the body fragments are everywhere on the ship considering that the T. rex was in the cargo bay.
When the Triceratops is attacking the InGen Site Base Camp, its tail is invisible when we see more dinosaurs released.
When the raptor traps Malcolm in the truck, the passanger door window has a spiderweb crack, but no hole from the inside. From the outside however, a small hole has suddenly appear in the center of the cracks.
When Kelly uses her gymnastics to kick the raptor through the window, there's an instance where you can see that it's a stunt double, and the double looks nothing like Kelly.
Also during the above scene, if you look in the background, you can see the asphalt road the vehicles are driving on.
When the male Parasaurolophus is captured, you will notice that some of the hunters tie its legs, and after it is tripped, you easily see that a hunter on the back is still looking upward where the Parasaur was, even though it was down already.
When Hammond is explaining Isla Sorna to Malcolm, we see the a film crew member's denim blue jeans reflected on the mirror of Hammond's desk when it goes from left to right when Hammond is in his bed.
When the rope unties from the tree Eddie Carr ties to, the three protagonists Malcolm, Sarah, and Nick Van Owen are seen falling, but they are visibly seen with crew-wires attached around their waists.
In the scene when the group is being attacked in the field by the Velociraptors, the one that turns around and screams then is eaten by the Velociraptor turns and screams before the raptor even jumps. An explanation is that he heard, and saw, the raptor in the bushes before it jumped. This theory is not proved or denied so it could still be a mistake.
As a further issue with the above scene, when the guy started screaming he still had a chance to run for his life but instead he waited until it was too late. Although even if he did run the raptor would probably catch up to him and he would die anyway.
When Eddie comes and pulls up the trailers, he tells Ian that Kelly is in the high hide, but the winch on Eddie's car is what was lifting the high hide up, although the winch was most likely only holding a portion of the high hide. Eddie could have clamped the high hide section onto a tree, there is no way a car winch would give enough wire to hang the high hide, there just simply isn't enough wire.
When Eddie climbs in the trailers to attempt to save Ian and the rest of the crew, you can see him put his hand on broken glass as he climbs in. How is it that there is no blood or injury?
How did Kelly get down off the high hide? It's possible one of the Hunters got her down.
When Dieter Stark was falling down the small hill, a hand pops out, to see it completely, go scene by scene and you'll see a blue hand stopping Dieter's hard fall. And he hits the camera when he stopped falling when the camera bounced.
When the parent T. rexes are on the sides of the trailer looking for the baby one of them roars and you see Sarah scream then the angle changes she looking out the window and she was quiet calm.
When the male T. rex closes his mouth after the bellow that caused Sarah to make the above scream, you can see the fabric of the animatronic folding. Real flesh such as that does not fold, it stretches.
When the T. rex slams the bus and some people fall out if you look closely at the passenger on the end that fell out you can see some wires holding him on his shouders!
In the last scene, the Stegosaurus herd seems surprisingly calm, despite the fact that they are roaming within meters of a carnivorous T. rex family though it is possible that the T. rex parents were probably taking care of the juvenile and ignored the nearby stegosaurs.
The Pteranodon at the very end is briefly shown landing on a branch like a bird. Real Pterosaurs could never do this, and though some smaller Pterosaurs might have lived in trees, they never could have landed like that.
During the final scene on the cargo ship, the Tyrannosaurus appears when Ian pushes the button to close the cargo doors, then disappears from all subsequent shots, only to reappear to be hit by the tranquilizer dart fired by Sarah.
When the Unlucky Bastard gets eaten by the T. rex, a cameraman's legs can be seen in the reflection of the store's glass.
When Ian, Nick, and Sarah are rescued over the cliff by the Hunters, a possible stage light can be seen in the background.