Nextcloud Sync App (Flatpak) in Fedora SilverBlue with Dark Theme ends up like this

You could check your systemd logs with sudo journalctl > logs.txt Search that file for your application name.

Otherwise try running the application from terminal, and view any logs that output.

flatpak run {app name}

You might need to add options for logging.

My guess is it’s missing some gtk assets.

Yeah, same on Arch. I just had to turn it off.