Hi I'm Pablo, one of the developers.
Unfortunately, I have no idea how to solve the issue with the collision boxes (mainly because I am in charge of the art of the game), but we had problems with them along the development of the project, so I think there is a problem with the generation of the trees and that is why it is probably more complex to fix than how it looks like.
Thanks for playing our game though, I hope you had a good overall experience!