Thanks for provided scene. It looks like, that this issue is linked to heavy use of Forest instances (Clone - Instance) in your scene.
Generally, we recommend to use Clone - Copy while a copy of the Forest object is needed as using Forest object in Instance / Reference mode may lead to unexpected results (like overlapping items). To fix your issue please select all instanced Forest objects and Make them unique. Attaching screenshot.
We'll keep looking into this issue to see what can be done to avoid similar kind of troubles.