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.
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)
When Littlefoot and the gang run away from Sharptooth after their sleep, Petrie is on top of Littlefoot's head. After the rest of the gang run into the crevice, we see Littlefoot being chased, and Petrie is not on his head. When Littlefoot does enter the crevice, Petrie is back on Littlefoot's head, but when Sharptooth breaks the crevice Petrie is not seen rolling down the hill with the gang. After Sharptooth is seen with its muzzle stuck in the now bigger crevice, Petrie reappears, but in the next shot, both Petrie and Ducky are gone.
Sharptooth's right eye is meant to be blinded by Littlefoot during their first encounter in the thorns. But you can clearly see Sharptooth with his eye closed as he looks for Littlefoot and Cera before it is injured.
The scene in which the baby pterodactyls fight over the cherry uses two backgrounds, one for the vertical pan, another for the horizontal. The two backgrounds do not match exactly; particularly, the sky changes color, and a knothole in the bottom of the screen disappears and then reappears.
In the final battle as Sharptooth and Ducky slide into the water, Littlefoot, Petrie and Spike are seen standing above them by the rock and Spike is looking down from Littlefoot's right side. A split second later when the camera cuts and shows the fronts of the characters, Spike is now on Littlefoot's left side.
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.