All flatpak updates are blocked if at least one flatpak is from GPG unverified remote
When one of the flatpaks is from unverified remote (there is issue with this on Fedora flatpak remote right now), gnome-software blocks update of the other flatpaks, even those that are from verified source.
If I do
flatpak update manually only those from the unverified remote are skipped.
Fedora flatpak remote could be added by
flatpak remote-add fedora oci+https://registry.fedoraproject.org, but it should be already available if you are running Fedora.
gnome-software version: gnome-software-3.32.0-6.fc30.x86_64
flatpak version: flatpak-1.2.4-2.fc30.x86_64