Near the beginning of the movie, when Grant falls asleep on the plane, he dreams of seeing a Velociraptor beside him. The mistake is that the raptor is like the ones encountered later on the island, with features such as small quils on its neck. However, he had not yet encountered ones like this, only the ones he had seen on Isla Nublar. In the commentary for the film, it is said that this raptor was "greyed out" in Post-Production of the film to attempt to correct this.
When the plane is flying through Isla Sorna, on a mountain you can see telephone wires.
In the Truck Scene, where Dr. Alan Grant and Eric Kirby are sitting in a water tank (truck) eating candy bars, they show Eric eating a "Crunch" bar with no wrapper, just in the tin foil. In the next shot you see him eating the same candy bar but the "Crunch" wrapper is now on. Then in the third shot it cuts back to Eric and the wrapper is gone and you only see tin foil again.
When Grant picks up the flask with the Tyrannosaurus pee, the container has no liquid inside it.
In the shot when the Raptors were running through the grasslands, if you listen closely, you can hear possibly a computer graphical sound as the Raptors run.
When the group was flying into the island, there's a shot of the plane flying in front of the cloud, and there's the obvious shadow of the helicopter that filmed that shot.
When Dr. Grant dives in the water after they're attacked, he has his watch on his right hand before he dives in, but in the rest of the shots of Sam Neill, he has his watch on his left hand.
Just after hearing the Spinosaurus roar, bright studio lights are reflected on the front of the plane when it is turning to take off from Isla Sorna.
If you look closely at the Spinosaurus and T. rex you can see that they have no throat, just a back plate were the throat should curve down the neck.
When discussing the species of the dinosaur that had attacked them, Billy first guess is Suchomimus, but Grant tells him to think of something larger than that. Billy's next guess is Baryonyx. In reality, this should have been reversed, as Suchomimus was larger than Baryonyx.
In the scene where the group watches the video on Amanda's camcorder it show footage at the beach and then it shows Ben and Eric parasailing. In this part, the words said over the camcorder are noticeably different from the first scene in the movie where the footage was supposedly filmed.
Just after the crashed plane has been kicked by the Spinosaurus and stopped rolling, we see the Spinosaurus going towards the plane through a window. The Spinosaurus is not bending its head low in the shot, but its head is too high off the ground when it stands for this shot to be physically possible.
In the scene where Nash borrowed the cellphone from Paul Kirby, he had a shotgun on his back, but when he fell to the ground, he had a rifle, which then switches back to a shotgun before he gets eaten.
In the beginning where Billy is parasailing when the rope is being pulled, he puts the camera behind, but it just vanishes before he falls into the water.
In the extras, it is stated that Jurassic Park III was the first Jurassic Park film to feature Pteranodon, despite the fact that the reptile ultimately had a brief cameo in the last several seconds of The Lost World: Jurassic Park. What they probably meant was that it was the first film to give Pteranodon an important role, as in the aforementioned previous film it is only seen for the last few seconds and did not appear at all in Jurassic Park.
The bag separator becomes damaged in the ambush scene near the end.
During the first Spinosaurus attack, the plane hits the tree with the windows and seats upside down. In the next scene with Mrs. Kirby looking out the window at the Spinosaurus, the windows and seats are not upside down.