Applications like Discord and Slack have a feature where the application will keep running after you hit the close button. I’m noticing that if I close one of these apps, an invisible window will remain that blocks all my clicks in the area that the app was before I closed it. Opening the app again fixes it. This is true in both Wayland and Xorg modes and this is true with all extensions turned off. I’m on Arch with Gnome 48.2.
Edit: Couple more things about the behavior… if I position discord and slack side by side and close both to the tray, I will get two ghost windows, one for each. However, I only need to reopen one of the apps again for both ghost windows to disappear.