I run XFCE, but I think we might have the same issue. Please tell me if I'm wrong.
In my case it is the View menu. Sometimes opening it seems like it causes some invisible aspect of the menu to get stuck open. The View menu closes and disappears, but something else gets stuck in the process and it causes a strange floating invisible rectangle the size and shape of the closed menu that shows my background when other windows are on top of it.
It was hard to get a screenshot because most times when I take the screenshot the invisible menu disappears in the taken screenshot! But I caught it this time!
C'est ici! The incredible invisible floating menu!

I don't know how to reproduce it either. I say that I believe it gets stuck because somehow I got it unstuck yesterday after taking the screenshots and it disappeared. I think I clicked around in the Steam client and that fixed it.
Edit: I confirmed it is the View menu based on dimensions.
I think this might be fixed with today's beta client update :D
Thanks for the feedback @nightsky30, closing.
Nothing extracted yet.
Your system information
Sometimes, strange invisible window overlaps with some desktop icons.
I don't know, how to reproduce that, but i got some info from xorg:
xwininfo:xprop: