When Grandma Longneck states "Littlefoot is right. I'm sorry if this will be painful for you." she has Grandpa Longneck's coloration.
When Rinkus and Sierra are blown away by the Stone of Cold Fire's explosion, and they land in the cave in the mountain, their positions have been switched around.
The fiery comet which Littlefoot sees at night is now yellow instead of blue (although it remains blue during the song Beyond the Mysterious Beyond), the fiery pit which blows Littlefoot and his friends out of Threehorn Peak and the small boulder they stand on are entirely reanimated, the pillar of light at the very end is more shiny, and the late-1990's Universal Television logo is added right before the Universal Cartoon Studios logo (which is mysteriously sourced from The Land Before Time V: The Mysterious Island, judging from the last second of the end credits music being heard between both logos).
Like many dinosaur pop culture depictions, most of these dinosaurs depicted existed in different millions of years time (throughout different eras) and not altogether.
In the flashback sequence detailing why Pterano is met with scorn by the adults of the Great Valley, Grandpa Longneck explains that after the Great Earthshake, the adults communed and traveled together as a group, with no one's opinion outweighing the other. This contradicts with much of the "racism" expressed in the first Land Before Time film, in which many of the herds kept to their own kind.
While Pterano is flying with his henchmen after they had kidnapped Ducky, he clearly has a completely different color scheme. His skin is a greenish blue while in the rest of the movie, it's a brownish orange.