Incorrectly regarded as goofs: Many scenes contain grass. Grass didn't evolve until the early Cenozoic era, shortly after the dinosaurs died out. However, recent discoveries indicate that grass did, in fact, exist in at least the Cretaceous period. Naturally, according to science at the time of the production, it was still incorrect.
Anachronisms: Lemurs and all other primates did not co-exist with dinosaurs. Several other creatures are from varying epochs.
Factual errors: The main characters are iguanodons. Iguanodons actually had hard beaks for mouths, except when the film makers decided to have the dinos speak, the beaks just didn't work well with speech movements. So fleshy lips were modeled over the beaks for speech, and the beaks underneath act like pseudo-teeth in the final film.
Factual errors: There are many other inconsistencies between the fictional representation of dinosaurs in the movie and accepted scientific knowledge at the time the movie was made. It should, perhaps, be remembered that it's family entertainment, not a documentary.
Continuity: At one point during the migration, Aladar is talking to one of the lemurs who are riding on his back, but the other three lemurs are missing. In the next shot, all four are again on his back.
Continuity: In quite a few shots of the movie, Aladar's eyes turn from a bright green to bright blue and then back again in the next camera shot.
Continuity: When Baylene is running to jump in the lake at the Nesting Grounds, she is shown to run right near the water’s edge. After three shots, she is back where she started to run.
Factual errors: The Carnotaurs seen in the film were much bigger than their real life counterparts. In realty the were smaller than Iguanodon's (Aladar's species) whereas here they are made as large as some of the biggest Dinosaur predators (like Tyrannosaurus). This is presumably done for dramatic effect and wouldn't be the first time such a change has been made (the Velociraptors from Jurassic Park).
Continuity: When Aladar accidentally smacks into Neera's head after discovering the herd, she snaps at him and immediately turns away to continue on. However, in the next shot in which we see her from Aladar's point of view, she is just beginning to turn away.
Factual errors: Throughout the film, all of the Iguanodonts (including Aladar, Neera, Kron and Bruton) are shown running on all four legs. According to modern paleontological theories, however, it is likely they would've been able to rear up on their hind legs to run.