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.