Using mutter 3.20.3 on Fedora 24.

Steps:
1. Open app A on monitor 1 (e.g. nautilus).
2. Open fullscreen app B on monitor 2 (e.g. Remmina, gnome-terminal).
3. Open non-fullscreen app C on monitor 2 and place over fullscreen window. Everything is fine at this point.
4. Switch focus back to app A on monitor 1. At this point, B has risen to front and C is no longer visible.

I expect that C should remain visible on top of B. I usually use fullscreen because it simplifies/improves the UI of a particular program - e.g. in a Remmina session I want to see the full screen of the remote computer without scaling or cropping. It's very useful to me to have a fullscreen window be in the background of everything else.

In general, the stacking priority of a fullscreen window seems to be too high. In the previous example, it's also impossible to drag app A above app C. You can drag it onto monitor 2 and it retains focus, but it's not visible until you move focus to B and then back to A. (Then once A is above B, you can drag it back and forth between monitors and it will stay on top - the rules are inconsistent/unexpected.)