The gnome-software-plugin-flatpak was known to have issues in 3.26,
would you be able to try again with Ubuntu 18.04 + gnome-software 3.28 ?

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https://bugs.launchpad.net/bugs/1719985

Title:
  flatpak software is not shown in gnome-software

Status in gnome-software package in Ubuntu:
  New

Bug description:
  I installed gnome-software-plugin-flatpak which install flatpak and a
  few other packaged.

  After a reboot I opened gnome-software and at the top of the app under
  the headerbar I saw "Sorry, something went wrong" popup.

  I couldnt find any flatpaks shown in the software center.

  Is there something else we need to-do to get flatpaks working in
  17.10?

  Subsequently I can confirm that I can install flatpaks via the command
  line though using the flathub command line webpage.

  ProblemType: Bug
  DistroRelease: Ubuntu 17.10
  Package: gnome-software 3.26.0-0ubuntu2
  ProcVersionSignature: Ubuntu 4.13.0-12.13-generic 4.13.3
  Uname: Linux 4.13.0-12-generic x86_64
  ApportVersion: 2.20.7-0ubuntu1
  Architecture: amd64
  CurrentDesktop: Budgie:GNOME
  Date: Wed Sep 27 20:17:46 2017
  InstallationDate: Installed on 2017-09-27 (0 days ago)
  InstallationMedia: Ubuntu-Budgie 17.10 "Artful Aardvark" - Alpha amd64 
(20170926)
  InstalledPlugins:
   gnome-software-plugin-flatpak 3.26.0-0ubuntu2
   gnome-software-plugin-limba   N/A
   gnome-software-plugin-snap    3.26.0-0ubuntu2
  SourcePackage: gnome-software
  UpgradeStatus: No upgrade log present (probably fresh install)

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