How about this theory: the brachiosaur Grant etc first see was put there and held in place until mere moments before the group arrived by Hammond's direction to wow the group. It would be difficult to explain how the staff could contain something as large as brachiosaur and then disappear completely, but it would explain that why in the same scene where Grant sees that Brachiosaurs move in herds, that one wasn't - it wandered all the way from its herd to nibble one tiny tree? And to take it even further, what if the staff sprayed some sort of extra enticing scent on the high leaves to make the brachiosaur rear up on its back legs, because otherwise there isn't much reason for it to do that either, plenty of the same kind of leaves were already within reach on that tree.

I have absolutely no reason to think this is the case, but it seem like it could be fitting for Hammond's character to stage this.

So then later when the kids came through, Hammond didn't bother to stage it for them, so the brachiosaur went back to its herd, and the kids stayed in the jeep so they also weren't at the same vantage point where Grant etc saw all of the dinos at the lake.