Comment # 5 on bug 1137537 from Fabian Deifu�

Not a flatpak dev, so cant provide clarification on why it happens.
However the error occurs when using flatpak with the --system flag.
Check that by "flatpak remotes" and see if the option says "system".
To fix it delete the flathub remote "flatpak remote-delete flathub" and add it
with the --user flag "flatpak remote-add --user --if-not-exists flathub
https://flathub.org/repo/flathub.flatpakrepo".
I assume you previously also had to provide a root password when using flatpak.
That'll be gone too.
I don't know how to reinstall all apps as --user though. It would be awesome if
anyone could clarify that!