I’m running a fresh install of Fedora 42 Workstation on AMD CPU and GPU with the default DE - GNOME on Wayland
Here is a video of the issue - I chose netbeans (before the netbeans hate comes in - I don’t use netbeans by choice it’s for my uni class) because it is the easiest to replicate this issue with, in other apps it just seems to happen at random - even with non flatpak apps sometimes. I’ve had this happen before with the spotify flatpak and even the brave browser when using the file input dialog.
Things I have tried:
Setting _JAVA_AWT_WM_NONREPARENTING envvar to 1 for flatpak apps
Using x11 for said apps
Using KDE (Wayland) - surprisingly it doesn’t seem to happen there - but I want to use GNOME lol
Disabling extensions - they’re not the issue either
One thing I have noticed is when I press Alt+F2, type in lg, and check the windows section - the phantom windows are not there and undetectable by the hovering utility.
I’m running this same setup on my laptop and the issue is there too.
I’ve been having the same issue on a freshly updated and rebooted install of Fedora 42 since yesterday.
I was running some Python scripts with Tk windows (matplotlib and other gui) that displayed on top of the vscode window in the back. After they close, the space they occupied before is now unclickable in vscode. If I mouse over the old border I even get a window resize cursor, so something thinks the windows are still there:
I confirmed it’s not internal to vscode by running the python app through an external terminal which had the same result.
Since both vscode (an electron app) and tk run through xwayland, I tried another X11 app on top (xeyes). Same behavior when killed with ctrl+c in the terminal while over vscode, no issue when using x button.
Other xwayland apps on the bottom can also be blocked, like Anki 25.02.4 which uses Qt 6.6.2.
It does not matter if the bottom app is maximized or not.
Native wayland apps (firefox or gnome-calculator) cannot turn into ghost or be blocked by ghosts.
Blocking is restricted to the app that was under the app that turned into a ghost when it did.
Resizing the blocked app clears the ghost.
So it seems like the issue is X11 windows on wayland overlaying other X11 apps and then getting closed by anything but the x button. So maybe it’s a bug in xwayland or mutter related to cleaning up clients that died in an unusual way?
Steps to reproduce:
Open an X11 app (most electron apps like vscode, any qt app like anki)
Maximize it
Open a terminal
Run another X11 app through the terminal in a smaller window (xeyes works well)
Position the smaller X11 window over the bigger one and remember its position
Without minimizing either, go to back to the terminal and terminate the smaller app using ctrl+c
Observe the mouse cursor around the border region of the closed window, try to click where the window was
