The name of the Nautilus .desktop file has changed in 3.13.1 to org.gnome.Nautilus.desktop but the defaults.list is still referring to the old nautilus.desktop for inode/directory. This is causing gnome-shell to open directories with the wrong program here.
*** Bug 1105781 has been marked as a duplicate of this bug. ***
Fixed in shared-mime-info-1.3-7.fc21