Thank you for your post.
This issue only appear because the wall height is lower than the top of the window or door and can't cut the opening. We are looking at fixing this in the not too distant future but it hasn't been confirmed yet on when this will be.
What I would recommend to do is to manually edit the external skin (cladding in this case) down the required distance.
Would you be able to please let me know if this works for you?