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.
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 leaving after defeating the lizard men with Rick riding on the T. rex, Holly falls down backwards while they begin to walk away. The shot changes and Holly is back standing on her feet in the background, then the shot returns to close up and she's being helped up by Will.
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.
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 Dr. Marshall first sees the imprint that his lighter made in a rock, the lettering from the lighter can be seen imprinted on it in stone. Later when the T-rex actually steps on the lighter, the lettering is facing upward making it impossible to make an imprint on the rock.
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.
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.
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).
The goof item below may give away important plot points.
When Marshall and Holly jump back through the time warp at the end of the film, they are both obviously empty handed with no more back packs or bags or souvenirs of any kind. So how would they prove the the world they actually had the adventure and how did the dinosaur egg come back with them?