Looks like the old version of nautilus is still there.
Provide a Nautilus flatpak package on Flathub addresses getting the recent / latest versions of nautilus in flathub, but until then the 3.28 entry should be removed from flathub, as it’s confusing.
Additional info:
$ flatpak install org.gnome.Nautilus
Looking for matches…
Info: app org.gnome.Nautilus branch stable is end-of-life, with reason:
Nautilus is improving Flatpak integration before delivering it as stable, in the meantime the maintainers encourage you to test the development version from https://sdk.gnome.org/gnome-apps-nightly.flatpakrepo
Required runtime for org.gnome.Nautilus/x86_64/stable (runtime/org.gnome.Platform/x86_64/3.28) found in remote flathub
Do you want to install it? [Y/n]: ^C
$ flatpak remote-info flathub org.gnome.Nautilus
ID: org.gnome.Nautilus
Ref: app/org.gnome.Nautilus/x86_64/stable
Arch: x86_64
Branch: stable
Collection: org.flathub.Stable
Download: 5.9 MB
Installed: 18.7 MB
Runtime: org.gnome.Platform/x86_64/3.28
Sdk: org.gnome.Sdk/x86_64/3.28
Commit: ed5eb907cf9cd8ab7deff12891efd73699a647efe35d3843aadf594e87b51a4e
Parent: 70a3f2ec2e35e198874d63a732c9deb73adb1d36c3707f6b70b95a3e09ce764b
End-of-life: Nautilus is improving Flatpak integration before delivering it as stable, in the meantime the maintainers encourage you to test the development version from https://sdk.gnome.org/gnome-apps-nightly…
Subject: Mark nautilus as end-of-life in the repo (691dce1d)
Date: 2018-05-03 09:31:50 +0000