Goofs

When Ducky discovers Spike in his egg, Spike is portrayed as perhaps only two or three times the size of Ducky. However, the next shot a few seconds later shows Spike coming out of the bushes at a size much larger than that. (6 or 7 times the size of Ducky, a state in which he remains throughout the rest of the movie)

Littlefoot's leaf is too small in the second half of the movie. If it could fit on his head, he'd be almost as big as his mother.

Littlefoot's, Cera's, and Spike's eye colors change from their normal colors throughout various scenes during the movie, then back again to their original colors at least once each.

Littlefoot's mother's wound changes location, from her back to her neck, but Sharptooth clearly bit her back instead of her neck.

During the final battle with Sharptooth, Petrie is yellow, then black again as he falls into the water with Sharptooth.

Petrie and all other Pteranodons are portrayed as herbivores, while it has been proven that Pteranodons ate fish instead.

Pachycephalosaurus is depicted as a ferocious carnivore. In reality, it was a herbivore, or an omnivore that ate insects and other small animals at best. It is never explicitly stated that they would eat Cera, they were merely threatening her.

In spite of Grandpa Longneck having a credited voice actor, Bill Erwin, the character does not speak at any point during the film.

The dinosaurs existed in three different periods: Triassic, Jurassic, and Cretaceous. However, all the dinosaurs, as well as other prehistoric animals who appeared in this movie did not all exist in the same period. Triceratops, Parasaurolophus, Pachycephalosaurus, Tyrannosaurus, and Pteranodon were Cretaceous animals, while Apatosaurus (called Brontosaurus here) and Stegosaurus were Jurassic dinosaurs. Meanwhile, Dimetrodon, erroneously portrayed with a snake-like tongue, was actually a mammal-like reptile that lived way before the dinosaurs, more than 100 million years before this movie takes place.

Littlefoot's mouth doesn't move when he says "Cera, you're back!" while he and Spike are pushing the boulder onto Sharptooth.

On the 2003 DVD release, during Cera's conversation with Littlefoot, Ducky, and Petrie about her "brave" encounter with Sharptooth, the audio is sort of out of synchronization. However, that scene is corrected on the 2015 remastered DVD and Blu-ray releases.

When Cera gets separated from her family, she says "Daddy" but her mouth isn't moving.

At one point, Cera refers to Littlefoot as a "Flathead", but Petrie is the one who gave him that nickname, and Cera wasn't with the group when he did.