It sounds like you're trying to update system-wide flatpak packages as non-root. Most distros use polkit to allow you to update those without a password from the desktop (i.e. a local user), but usually require a password for remote users (like ssh). Just run as root: "sudo flatpak update".
You could also migrate to a user flatpak installation instead a system-wide one. That's what I've done. IMO that's how it should be done, but that's not the default on most distros for some reason.
Tbf, this is something that only some distros do. Those distros should be reprimanded for handling home directories with the tmpfiles system, not systemd.