You have a mod conflict. That is to say, somewhere you have a mod that says that tree should be there. That is why you aren't seeing it there in the Construction Set, but you are seeing it there in-game.
You could figure out what mod is doing it by disabling all your plugins, then re-activating them one at a time to see if/when the tree comes back.
You could then edit that mod to not include the tree, or move that mod higher in your load order so that this mod's removal of the tree is the change that sticks.
This is the "cleanest" way to fix your problem, because it will not affect your saved game. It will require you learning a little bit and spending some time.
Or, you could just use the console and be done with it in 2 minutes or less:
1) Go to the tree in-game.
2) Open the console with the tilde (~) key.
3) Click on the tree. At the top of your screen, you will now see " " and an 8-digit hex code.
4) Type "disable", without quotes. Press Enter.
5) Tree is gone. *poof*
6) Resume play.
This option is permanent to your saved game unless you undo it later with the console. On the bright side, it does not require you learning anything about how to manage your load order or find an object in the CS.
Take your pick, and best of luck!