I've noted that sometimes the trunk of a tree can be seen through/on top of the branches of a tree that should obscure it, while most of the time the trunk is obscured. Then I noted that a see-through tree had a feather at its base, removed the feather, and found the display order return to normal, i.e. the trunk of the tree behind it became obscured again. Shortly after that I saw another see-through tree, and yes, it has a feather at its base.
If it's of interest I saved and copied the save just before removing the feather from the first tree.
The issue has no game play effects as far as I know, so it's only a visual oddity.