Jo Jo retrieves the diary and stows it on his chest under his shirt, thereby soaking his shirt. As he's then returning to the other three boys, his shirt is dry.
When the boys pull the boat to the shore the evening of the dinosaur battle, the opposite shore of the river looks completely different then it does when the two dinosaurs fight, this happens again the next morning after the battle.
During the Pteranodon attack an oar for the boat is lost and it floats away, however after the attack ends, all four are instantly back and the lost oar is already being used again.
The film shows the giant carnivorous bird Phorusrhacos (called by its outdated name "Phororhacos" in the film) living at the beginning of the Paleogene period after the dinosaur's age ended about 66 million years ago. But in reality it was far more recent, living about 20 to 13 million years ago, after the Paleogene. It is possible that the filmmakers confused it with another famous giant prehistoric bird, Gastornis or Diatryma, which did live during the early or middle Paleogene and was also commonly but erroneously depicted as a carnivore during the 20th century.
The geological timeline in the boys' notebook mistakenly places the Ceratosaurus in the Triassic period rather than the Jurassic. Interestingly, one of the dinosaur sketches shown off at the beginning has the opposite error, it places the Ceratosaurus next to a Cretaceous armored dinosaur.
Ceratosaurus is erroneously depicted with what looks like a small thumb. Though the real animal did have a vestigial fourth finger, it was located on the outside of its hand, not on the inner edge.
During the dinosaur fight scene there is a moment when two of the four boys turn and face the camera, the complete opposite direction that the battle is happening.
At certain points during the Ceratosaurus' fight with the Stegosaurus, the support rods keeping the Ceratosaurus model steady can be seen seen behind its legs.
The sound is out-of-sync during the stegosaurus examination scene. Most noticeable when the boys are measuring the length of the dinosaur.