Hi, I'm using Mobian (PinePhone) with Debian bookworm arm64 repositories and see similar issue using gnome-software in Phosh.
There are listed updates, but if I click on 'Reboot and update', then error message is shown 'Unable to install updates: Prepared update not found: /var/lib/PackageKit/prepared-update'. Change to /usr/share/polkit-1/actions/org.freedesktop.packagekit.policy mentioned by Elias fixed updates. This is regression happened with update to packagekit 1.2.4-1. There was no such problem with packagekit 1.2.2-2. -- Best regards, Andrey Skvortsov