In some apps such as Oracle VM and MySQL Workbench right and bottom parts are unclickable. They’re rendered as normal, but all the clicks in 20% of the right screen go through the window to whatever is behind it. Even minimize and close buttons are not responding. Resizing the window helps a little, but even then part of window (just a smaller one) remains unclickable.
I’m using Wayland + Gnome and I’m not sure what part of system is to blame for the problem. May be the applications themselves are poorly built, I haven’t find any similar problem in the google. There were ones with AnyDesk, but I’ve never used it.
What version of mutter and gtk do you use?
I actually have the same issue on my Desktop. Running Arch Linux x86_64, GNOME 46.1 / Mutter, kernel 6.8.7-arch1-1. Started happening as of a month or more ago.
GNOME 46.1 / Mutter
What is the exact version of the mutter and gtk package and have you restarted your session since the last update?
I don’t know what my mutter and gtk versions are, but the setup is almost the same as maxrdz’s. Arch, gnome 46, kernel 6.8.4. Can’t say if it’s an old issue, because I’ve only installed arch around a month ago
Update: mutter is 46.0-3; gtk2 is 2.24.33-3; gtk3 is 1:3.24.41-1; gtk4 is 1:4.14.2-1
But I think the problem had been happening even before I updated from Gnome 44 to 46
Try updating gtk to 4.14.3 or mutter to 46.1, either should work, but the gtk side fix also fixes issue with resizing the window.
Thanks, I’ll try.
But I also wanna clarify that there’s no issue with resizing the window
gtk4: 1:4.14.3-1
mutter: 46.0-3
gnome-shell: 1:46.0-1
Have you restarted your session since the last update?
I sure did.
Interestingly, as soon as I’ve updated to latest gnome (along with some other updates via pacman -Syu) the root started behaving bizarre. It didn’t accept my root password thru console, even though it was correct. So I had to restart the system to fix it
The root password issue happened to me too a while while ago, and was also fixed through a restart (if I remember correctly. this was months ago) 
I think clicking on window options (right click on top window bar) and picking ‘Restore’ might help