If you do the "good" route, the tree in Whiterun is supposed to disappear and be replaced with the sapling. As it stands, the tree in Whiterun doesn't disappear, which causes it to look weird. If you do the quest the "bad" way, there are no problems, but I don't want to do it that way.
Interesting, that makes sense, but I never even questioned that the quest was broken. I just assumed the old dead tree always stayed there, even if you brought the sapling. This would be nice to see fixed. I'm sure it can be fixed with a console command on PC, if the assets are already in the game.