Doesn’t sound like a Flatpak issue to me.
You mentioned that you tested:
- WSL with Ubuntu and X11
- Fedora with Wayland
So, this could be just an issue with your Wayland code (assuming you have Wayland support), like not releasing the window after closing the game…
So, it would be good to first test if this is reproduceable under Fedora with X11 as well.
If you want to check under Flatpak as well, you could use the arguments --nosocket and --socket to force one system.
For example,
flatpak run --nosocket=x11 --nosocket=fallback-x11 --socket=wayland APP_ID
would give the app only access to the Wayland server, while
flatpak run --socket=x11 --nosocket=fallback-x11 --nosocket=wayland APP_ID
would only provide the app with X11.