Please accept my apologies for my ignorance, as I am the newest newbeee around FSDreamTeam but, my own experience has indicated the problem you describe (trees in taxiways, etc.) is most often an AUTOGEN situation. I personally keep the Autogen slider to the extreme left, but then I run a lot of 3rd party scenery which provides it's own stuff.
In the case of sceneries which I have made (really poor efforts when compared to FSDT), I always start with an "Exclude" polygon which removes the autogen items within the confines of my scenery/airport.
Perhaps it could be caused by your Autogen parameter in your display/scenery control screen.
In any case, that's what I've observed. I'm sure others much more experienced will pitch in.
best of luck