Inconsistent flatpak update information

I run flatpak update --noninteractive automatically every night (from a cron script, run as root). Currently, if I run flatpak update as root it tells me there’s nothing to do.

If, however, I run flatpak update as an unprivileged user it tells me:

Looking for updates…


        ID                         Branch   Op   Remote   Download
 1.     org.gtk.Gtk3theme.Breeze   3.22     i    flathub  < 192.5 kB

Proceed with these changes to the system installation? [Y/n]: n

Running flatpak list as either root or an unprivileged user I don’t see org.gtk.Gtk3theme.Breeze listed as an installed flatpak.

Even more confusing, if I run plasma-discover under KDE as an unprivileged user it shows me a long list of the installed flatpaks and says they need “refreshing”.

How can I know if there are really updates available, and how can I reliably automatically install them?