While inside the Site-B main buildings, Billy uses his flash to photograph the dinosaur incubation tanks. Any photographer with a modicum of expertise would never use a flash when photographing a reflective surface (i.e. glass or water).
When Grant asks Billy how he would classify the Spinosaurus, Billy says, "It's a super-predator," and immediately suggests Suchomimus. Grant says, "Think bigger," and Billy suggests Baryonyx. In reality, Baryonyx was only about 2/3 the size of Suchomimus, which in turn was only about 2/3 the size of Spinosaurus - not nearly big enough to be a super predator. Regardless of that fact, Billy still got his dinosaur sizes badly out of order.
In one sequence, the Spinosaurus, whilst pursuing the main characters, smashes through a huge metal reinforced fence to get to them. Seconds later the main characters run in a small wooden hut and the Spinosaurus isn't able to break into it. How can it smash a steel fence open yet not be able to even slightly damage a wooden hut?
When Billy is about to jump off the bridge para-sailing his legs aren't secure with the straps, meanwhile Professor Grant is chasing him to stop him. But a second later when he is standing at the edge of the railing his legs are properly strapped. He couldn't secure himself with the straps in less than two seconds.
During the opening scene of the movie while Eric and Ben are para sailing, Ben starts to film with a video camera. While videoing the tugging begins, the next scene the camera is gone, but the next its back again. After this Ben slides the camera to his side and the camera disappears out of his hand.
When Ellie is walking toward Alan with her toddler, her shirt gets pulled a little bit of the way up her belly and then it falls again. When she's by Alan, her belly is covered. But at that moment as the scene changes, Ellie's belly button is showing.
When the Spinosaurus is trying to attack the characters we see a white damaged airplane. When the Spinosaurus starts to crush the plane we see a brief green model of the plane being crushed with no window holes and a few cables inside visible. This might have been a second dummy airplane to prevent destructing the original.
If you pay attention to the shadows when Dr. Grant is looking through the busted, dirty windows of the jeep before the group enters the compound, you can see the shadow of the tracking camera/crew briefly pass over the far interior of the vehicle just under the window and across the wheel well Grant is passing.
Although the depiction of the Pteranodon showcases several inaccuracies (such as having teeth, being able to grab things with their legs, and being excessively aggressive), which, being genetically engineered clones, can be explained, one detail still counts as an error. Namely, no matter how strong these creatures are, they could never lift up and carry a human boy the size of Erik. They would simply plummet towards the ground, since these animals needed to be extremely light-weight in order to stay aloft (a real-life Pteranodon would weigh less than preschool child). Thus the Pteranodon's anatomical inaccuracies notwithstanding, the sequence in question very nearly breaks the laws of physics.
When the Marines are disembarking the amphibious vehicles, one is seen getting off with his finger on the trigger of his rifle. Soldiers are specifically trained to keep their fingers off the trigger of their weapons to avoid accidental discharges, especially during the rapid disembarking of a vehicle.
When leaving the Island they are departing on a SH-60B Helicopter, the interior of which is nowhere near quiet enough for them to hold a conversation, nor laid out for them to be sitting in that configuration, especially with someone is being medically evacuated.
As the aircraft approaches the island, after air traffic control warns the pilot about violating the restricted airspace, Mr. Udesky correctly turns off all the audio switches on the panel for the King Air's radios. However when he leans back in his seat, looking over his left shoulder the airspeed indicator reads ZERO (12 o'clock) position. This wouldn't be the case if the plane were flying.
There are numerous instances where dinosaurs are portrayed in a manner inconsistent with widely published dinosaur hypotheses. These can be explained within the movie's world as errors or deliberate alterations by the characters who made the InGen cloning process.
There are numerous inconsistencies between this movie and the others in the Jurassic Park series. However, since they do not compromise the movie's own internal structure they cannot, legitimately, be classed as goofs.
While celebrating Eric's return, Eric explains he followed Mr.Kirby's cell phone jingle. Then they turn around to see a Spinosaurus standing there. It would have been impossible for the Spinosaurus to have gotten there unnoticed since a T-Rex creates impact tremors with every step when it walks and a Spinosaurus is bigger, according to Grant, than a T-Rex. It is also impossible for it to have been there the whole time since no one seemed to notice it standing there.
The "metal" wire ropes at the barrier fence where Alan and Eric reunite with rest of the survivors are obviously sash cords spray-painted gray. This is even more apparent when Alan and Eric run through the hole in the fence and the dangling ends of the broken ropes can be seen flopping around as they accidentally make contact with them.
The computer-generated Spinosaurus does not correspond with the practical version in terms of size. Compare the shots practical version holding Nash (the black mercenary) in its jaws to the shot of the computer-generated version trapping him under its foot and delivering the final bite. The CG creature looks nearly twice as big as the practical one in that shot.
After escaping from the spinosaurus and deciding not to drop the raptor eggs, the main characters go down the spiral staircase. Right before the metal stairs they find below break under the weight of Dr. Grant, the camera pans down the stairs and the clean cut where the stairs are about to break can clearly be seen two stairs down. The camera pulls back, and clean cuts can also be seen on the railings of both sides of the staircase just where it breaks.
When the man and boy begin para-sailing in the opening sequence, as they lift off from the boat an overhead shot looks down at them with the boat almost directly below them, but the boat is not moving and has no wake.