Got the same issue on Fedora 38 Budgie, where this happens to the Nemo filemanager window.
It started for me with the mutter-44.1-1 update on the 28/4, which broke several themes like Graphite, Orchis & Qogir and probably many others. There were issues on the previous mutter version to, the black frame was not there, but noticed i had to click very far outside the window border, to activate any window below the Nemo filemanager window.
The reason i think its caused by mutter, is that i tested the the mutter-44.1-1 update, the night before it was pushed with the F38 system updates, but had to roll back because of this issue.
On Budige i am now using the default Materia theme without any issues.
I’m seeing the same issue here too. I’m running Fedora 38 / Gnome 44. The timing shared by boxjellyfish lines up with my experience as well.
Starting today, the issue seems to fix itself when I lock the screen or let the system go to sleep, but it’s only one program at a time. At the moment I’ve seen the issue in Steam / Steam games, Signal, and Librewolf. The most persistent one is Signal, even when it automagically fixes itself it will come back if you re-launch the program where the others do not (so far).
Not go back to default themes - completely remove the config.
I went back in the chat log and the user "unlinked the ~/.config/gtk-"* (I assume this is where it’s placed) which fixed the issue (they also tried just switching back to Adwaita and had the issue still).
Generally, if you’re getting graphical “weirdness” with Gnome, blowing away all extensions and custom theme config is the first step (in the Extensions app there is a toggle for disabling extensions which makes that part easy). Then raise a bug with the theme/extension provider.