When Grandpa Longneck fights Chomper's Mom in the movie Petrie flies by distracting Chomper's Mom in order to lure her away from Grandpa Longneck but in the next shot after luring Chomper's Mom away from Grandpa Longneck Petrie turns into his mother.
When Ducky laments the loss of her family's egg, she describes it as being special because of its unique coloring and the fact that "there wasn't another egg like it in the whole world". When they later find the egg back in the nest, it looks exactly like the others, with no attempt whatsoever to make it remotely distinctive.
Chopper may be a baby, but being a T-Rex means he would've been a lot larger than he is. Tyrannosaurs were actually the largest of all dinosaur hatchlings, so the newly-hatched Chopper should've been slightly bigger than Littlefoot, not the size of Ducky as depicted in the film.
During the "Eggs" song, Ozzie refers to himself as a Struthiomimus (his species) instead of egg-thieves as constantly described in the movie. It would be millions of years later before the name is actually given to the dinosaur.
Like many dinosaur pop culture depictions, most of these dinosaurs depicted existed in different millions of years time (throughout different eras) and not altogether.
All the characters refer to the land outside the Great Valley as "The Mysterious Beyond". However, in the first movie, they all migrated to the valley from there. With most being adults, particularly Littlefoot's grandparents who spent most of their lives outside the valley, it makes no sense that the dinosaurs act like they don't know what's out there.