When I try to install software using Flatpak I get this error:

Warning: Failed to get revokefs-fuse socket from system-helper: User flatpak does not exist in password file entry

The installation succeeds anyway, though.

This issue seems to be related: https://github.com/flatpak/flatpak/issues/2959. It seems like a flatpak user needs to be created when you install Flatpak.