After the dinosaurs are on the island, they see that the path they crossed to get there is gone, so they have no way of getting back. Then when they call their parents a little bit of the path and some rocks (that weren't there before) suddenly reappear. Then when they sail back on the log about half of the path is restored.
When the traveling dinosaurs see the skeleton of the duckbill, the shot changes to a view from above. There you see the duckbill's footsteps. If he had turned into a skeleton that means he had been dead for a long time. There is no possible way his tracks would still be in the sand. In addition, his footprints show only two fingers while the bones have three fingers.
When the dinosaurs see the dead duckbill on their way to find food, Littlefoot's grandfather says "Don't you see." while Cera's father is standing next to him. In the next shot he is standing by Grandfather's tail. In the shot after that he is right next to the skeleton.
When the dinosaurs go on the cliff to avoid being splashed on by the huge wave, you can see that there are many brown rocks near the edge of the cliff where they are standing. The shot changes to an overhead view and now one gray rock is the only rock anywhere near the edge.
After Littlefoot and Cera's fight, Cera's dad says that each herd is on its own. This shocks the little dinosaurs and they gasp. Notice in this shot that though the dinosaurs move, their shadows don't. Petrie doesn't even have a shadow.
Littlefoot's Grandmother's neck is always beige throughout the movie. When Grandmother and Grandfather have a chat about Littlefoot and his disappearance, Grandmother's neck is suddenly dark green and sort of glows.