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.
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.
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.
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.
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.
The Carnotaurs seen in the film were much bigger than their real life counterparts. In reality the were smaller than Iguanodon (Aladar's species), whereas here they are made even larger than some of the biggest dinosaur predators (like Tyrannosaurus). This was presumably done for dramatic effect and wouldn't be the first time such a change has been made (the Velociraptors from Jurassic Park (1993) are also several times the size of the actual animals).
Both Aladar and his newborn child urinate on Yar after hatching. It is doubtful dinosaurs could urinate like this. Like their modern relatives, they most likely excreted a substance called uric acid, which wouldn't exactly look like mammalian urine, as seen in the movie, more like bird droppings.
The small, lizard-like Longisquama is depicted as a chameleon that's able to glide through the air with two rows of elongated scales coming out of its side. In reality, it most likely wasn't a chameleon-like animal and only had a single row of spikes on its back, meaning it couldn't glide. It also lived in the Triassic, well over 100 million years before the movie's timeframe.
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, if they chose.
Lemurs and all other primates did not co-exist with dinosaurs, but first appeared millions of years after the dinosaur era. The directors knew this, but felt the real mammals of the Cretaceous (the era in which the film takes place) were "hideous", thus supplanted them with "cute" mammals.
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.
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.
When Aladar goes back to rescue the herd. He exits the cave and its night time but the cuts of the herd before and after its day time.
When the Oviraptor runs across a log, its shadow is clearly just a darkened, oval-shaped blob that's too big for such a small animal, rather than a realistic shadow.
In one scene where Zini is trying to wake up Aladar by pulling on his eye, Aladar's sclera appears black, as the white of his eye had not been rendered. Shortly after, the tail of one of the lemurs clips into his side.
Many of the reptiles depicted (eg. Brachiosaurus, Iguanodon, Styracosaurus) did not live in the same time or place.
Throughout the movie Eema is about the same size as Aladar and Neera. But in the final scene when the dinosaurs are cheering for their new home (about 1h14m in) Eema stands alongside Aladar and Neera and is suddenly 3 times bigger than them.
The movie takes place in prehistoric North America, yet the Carnotaurs, the main antagonists were actually South American dinosaurs. The characters do claim that they haven't been seen "this far up north" before, however this doesn't rectify the mistake, since North and South America weren't connected back then. The Carnotaurs would have had to swim through the sea to reach North America, which would have been impossible.
The opening scene takes place in North America, yet several animals are present that belonged to other continents. The Oviraptor, the dinosaur that steals Aladar's egg, was native to Asia, while the large amphibian Koolasuchus only lived near the antarctic circle.
Zini calls his Dad Yar by his name Yar instead of Dad. Suri calls her Uncle Zini just Zini instead of Uncle Zini.