When Dr. Marshall is being chased around by the T-Rex in the desert. At one point it picks him up by his backpack and rips it apart and destroys it. He doesn't have it for the rest of that part. Then when they are climbing the volcano, he has it again on his back.
When Marshall examines the lighter imprint in the beginning of the film, the hinge for the lid of the lighter is on the right side of the "Big Cat" text. When the lighter is crushed by Grumpy, the hinge is on the left of the text.
When the group confronts Enik, Will takes off his necklace and hands it to Holly. When Will and Cha-Ka arrive at the village, Will is wearing the same necklace. Will and Holly do not come into contact or close proximity afterward, so Holly couldn't have returned the necklace.
When Dr. Marshall gets dressed the morning after his bug bite, he puts on a shirt. When he strips down for his 'dance' number across the pterodactyl nesting grounds, he is wearing an undershirt. He also has a bandanna on his head that he didn't have before the scene or after.
During the rescue attempt when Holly is in the cage, Will is lying on the floor and trips a Sleestak over. The shot then goes to Rick and Holly swinging away from him revealing only Will at the edge of the pit, however the next shot shows Will pushing the Sleestak he just tripped into the lava.
As the main characters leave the jungle and walk into the desert, Holly says,"This must be the main entry point into this world". There is either a CH-53 "Super Jolly Green Giant", or a CH-3E "Jolly Green Giant" helicopter stuck in the sand. It has 6 main rotor blades and 5 tail rotor blades, but the real CH-53 has 4 tail rotor blades and the CH-3E has 5 main rotor blades, so either way it is not correct.
When the team first arrive in the land of the list and meet the primates, Holly says she worked at Manchester zoo primate house.
The originator of this factual mistake is in error, for there IS a Manchester Zoo, and not as they otherwise claim.
The large plastic jug that Dr. Rick Marshall had the dinosaur urine in was not seen in the cave where they found the dead people nor was a bucket. They didn't bring it with them. They did show a pile of assorted junk in the cave. Perhaps he found them in there although it's never seen in cave. Even though a hadrosaurus is a 25' herbivore they were thought to be aggressive and fought for mates so seems likely if an unknown creature was messing with them they would injure him at least..
Just before the Allosaurus shows up, we see a closeup of Holly's video camera. She is supposedly recording the dinosaurs eating out of the ice cream truck, yet the LCD screen is completely off and so is the "recording" light (both of which would be very visible on a Handycam).
At the end, when Will is talking while surrounded by the women, his lips do not always match to what he's saying.
Will says his banjo has 4 strings. It obviously has 5 strings.
Dr. Marshall states that the T-Rex had poor depth perception. However, in reality T-Rex is believed to have had great depth perception.