Please note: I had to report this bug into Red Hat Bugzilla due to larger attachment size limits there. Please see the full bug description and attachments there:
https://bugzilla.redhat.com/show_bug.cgi?id=1283689

I copy the original description here:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
I have two apps on my current workspace, Firefox in front, Terminal in back. When I switch to a workspace below, Terminal is temporarily rendered as a top-level window, during the transition animation. When I switch back to the original workspace, I see again Firefox on top. This is quite jarring and uncomfortable, because the windows jump and flash every time I switch desktop.

This only occurs if I'm using two monitors and there's some window on the secondary screen. If there's no window, the bug doesn't occur.

I tried to capture a screencast. Due to low framerate, it's not that much visible, but in real conditions, the issue is much more obvious. In the video, please note that when Firefox is on top and I switch workspaces, terminal is temporarily rendered on top.

This only happens with Wayland.

Version-Release number of selected component (if applicable):
gnome-shell-3.18.2-2.fc23.x86_64
mutter-3.18.2-1.fc23.x86_64

How reproducible:
always

Steps to Reproduce:
1. have two monitors, open Firefox+Terminal on primary screen and 1 app (hexchat, gedit) on secondary screen
2. make Firefox foreground app
2. switch from first workspace to second workspace, see that the background app is rendered as foreground app temporarily
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~