Science Marches On: Oviraptors were assumed to be nest raiders when they were first discovered, and named appropriately. Then it turned out, thanks to new technology, that the eggs they are usually found with contain baby Oviraptor. This is more a case of They Just Didn't Care, since this discovery was made several years before the movie. However, this discovery does not completely rule out the inclusion of eggs in an Oviraptor's diet. Recent research has however, revealed Oviraptor nests, containing embryonic bones from other species, as well as its own, suggesting that it may have eaten eggs after all...
The Pteranodon, despite being accurate for its time, is shown dip-feeding (snatching food from the water with its beak) and rearing its young like birds. In recent years, its been proven that Pteranodon would be more likely to catch food by swimming (its prey was noted to be rather small, so dip-feeding would have been impractical) and that baby pterosaurs would have been able to take care of themselves when they were born.
What Could Have Been: The original goal was a film without dialogue but with a narrator; then the writers decided it would have been too docu-like without talking animals.
Which is nothing compared to some of the other rumored plans for this film. Imagine a Paul Verhoeven Disney movie.
Why imagine when you could just watch Starship Troopers (co-produced by Disney's Touchstone Pictures arm and (outside North America) released by Disney's Buena Vista)?
Also, the villain was actually originally going to be a Tyrannosaurus rex instead of a Carnotaurus. This is still evident in the final film, due to the Carnotaurs being essentially the same size as adult Tyrannosaurus, thus making them two to three times bigger than real life Carnotaurus.
An early draft had Aladar named Noah, and traveled with Zini and his two grandparents. The world was much more lush, and finding food and water did not seem to be a big problem as it is in the final film. Some scenes included Kron leading the herd across a river swarming with predators, and Aladar's grandparents letting themselves be killed by the Carnotaur when they grow too weary to keep up with the herd.
There would've been a scene depicting Neera being attacked by raptors while trying to save the orphans, and being saved by Kron. And we would've seen the Stygimiloch (the Pachycephalosaur that we see the Carnotaur eat while Aladar hides from it) collapse from exhaustion.
Another more light-hearted scene would've had Eema stubbornly give up the journey and her position as the group's guide, only getting back up when Yar was offered her job.
An alternate scene showing the Carnotaurs scaring off the raptors, who are still eating the Gallimimus they've picked clean in the final cut.
An abandoned backstory for the Nesting Grounds, in which Eema tells the story of Old Gatoma, a long dead Iguanodon who was the first to find the valley and led the herd to it every year.
Concept art suggests Url would've been much larger, about the size of Eema even! And there would've been more sauropods in the herd.