Using an XWayland app with fullscreen mode, for example VLC, other windows will always be behind. This is different to Wayland based fullscreen apps or in an X session.
I tried to reproduce today with kwrite/xcb and was able to move other windows on top of it. Could you please xprop and xwininfo an affected window? I assume it's not a normal window but override redirect.
*** Bug 372514 has been marked as a duplicate of this bug. ***
Triggered the problem today with kate --platform xcb
That one was tricky: the problem is that the stacking order for X11 fullscreen windows does not depend on the active window but on the most recently activated client. The most recently activated client is a concept I thought we do not need for Wayland. On X11 when activating a window a request is sent to the window and it takes focus. So KWin only marks it in the most recently activated client list and removes it from there when it actually gained focus. Have a patch for the problem, now thinking about a unit test ;-)
Git commit dcbfa0869b3604d0636e4b470f03ac9bcca6da77 by Martin Flöser. Committed on 23/07/2017 at 09:50. Pushed by graesslin into branch 'master'. [autotest] Add a test case for X11 fullscreen windows when an Wayland window is there KWin cannot handle the layering correctly when a Wayland window is active and there is a fullscreen X11 window. This test tries to simulate the situation, but it does not show it. Nevertheless it's a good test, so let's add it. M +88 -1 autotests/integration/x11_client_test.cpp https://commits.kde.org/kwin/dcbfa0869b3604d0636e4b470f03ac9bcca6da77
*** This bug has been marked as a duplicate of bug 439405 ***