There was a different ending; there's several pics on this page already of clips from this. Also, if you are lucky enough to own the soundtrack (I do, yay me!), you can actually hear where the missing scenes went. I posted a picture analysing the soundtrack ages back; I think it's on this page, but for sake of ease, I'll retell it here. Judging by the way the music goes (in other words, where the music is played in the film);
The alternate ending starts immediately after the GOF splits in two, and Cera leads Spike, Ducky & Petrie into the "Mountains That Burn". Immediately after Ducky and Spike seperate from the group, we return to Littlefoot climbing the hill, where he hears his mother's voice calling him. Littlefoot sees her shape in cloud form, and follows her as she leaves, ending up on a rocky plateau. The sun comes out through the clouds, revealing the Great Valley below. Littlefoot, realising he's found it, happily jumps through the upper part of the waterfall. However, he realises that Cera will be leading the others the wrong way, and so he goes back to get them (rescuing them, and heading to the large lake). At the lake, they hear Sharptooth moving over the mountains. Littlefoot realises that he will follow them into the valley, and thus they plan to get rid of him (there's a good minute or so of music here that's not in the film; presumably this scene went longer). Their plan is successful, despite Petrie getting pulled down with Sharptooth as he falls. However, he is alright, and Littlefoot leads the others from the rocky point above the lake to the entrance to the valley.
You can see evidence for this in the film. When Littlefoot is on that rocky part at the end, and sees the ghost of his mother, look at his surroundings. Not only can you see the lake below him, but above that is the ramp and rock that they push on Sharptooth. When he runs after her, you can see he's running up the same hill he was going up when Cera deserted. Finally, when Sharptooth is seen climbing around the lake, you can see green plants growing on the right side of the screen; where the Valley is. In addition to this, the air is of a deeper colour, compared to the barren colours of the rest of the film.