Going to share my reply to a similar question:
Did Xwayland Video Bridge get installed onto your system? After something installed it in a recent update for me, I started having similar issues. Regularly lost the ability to click on the desktop, or click on application windows that weren’t in focus, but no problem using the launcher or switcher.
Next time you notice the problem, try showing the desktop, moving your mouse to the very top of the screen, and right-clicking. In my case, this brought up the kind of context menu usually seen on window title bars, even though no title bar was visible.
It turns out, this was some ghost window created by Xwayland Video Bridge. If you close the window from the context menu, the issue will be fixed until Xwayland Video Bridge gets started and the computer goes to sleep again.
In the end, I just uninstalled Xwayland Video Bridge. All it does is allow X11 apps to record/stream content in Wayland windows, which isn’t functionality I really care about. I don’t know if a fix is forthcoming, but I’m fine without it.