I've seen this same issue in earlier one think I seen it going on in the current java development versions also.
If you notice there is a tree in the picture that the outer edges and branches are at a different height that the middle of the tree.

It looks like the tree was created before the land was lowered in that area. I've also seen area where it looks like someone just took a knife and cut the side off of a long strip of forest. This is on new maps.