Flatpak permission issues

Lately, I've been having some issues with running most of my Flatpak apps.
It seems to be related to Vulkan and the inability to create files in /usr (which it shouldn't).

I've tried repairing flatpak, tried reinstalling apps with system or user with no luck. I tried rolling back to F40 with no luck then rebased to stable again. Everything should be up to date (using ujust upgrade). I've tried researching with no luck, I might have to wipe and install bazzite again but I hope I don't have to go that route.

Here's an example where protontricks fails to run:

 Nov 19 19:01:57 bazzite systemd[2603]: Started app-com.github.Matoking.protontricks@d4ef2dd0cb9d47dfbba376868b1f2061.service - Protontricks.
Nov 19 19:01:57 bazzite flatpak[36337]: bwrap: Can't mkdir /usr/lib/extensions/vulkan: Read-only file system
Nov 19 19:01:57 bazzite flatpak[36332]: error: ldconfig failed, exit status 256
Nov 19 19:01:57 bazzite systemd[2603]: app-com.github.Matoking.protontricks@d4ef2dd0cb9d47dfbba376868b1f2061.service: Main process exited, code=exited, status=1/FAILURE
Nov 19 19:01:57 bazzite systemd[2603]: app-com.github.Matoking.protontricks@d4ef2dd0cb9d47dfbba376868b1f2061.service: Failed with result 'exit-code'. 
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