since some versions, the PackageKit-gnome software update UI displays updates in bundles; if I have e.g. a NetworkManager update which would require packages network-manager-glib, network-manager-devel, ... to be installed, they're shown under an expander, which I think is a really good idea.
Though, if I deactivate the toggle button near the unexpanded package bundle, I'd expect all the updates inside it to be ignored. The way it currently works is it ignores only the first one in the bundle.
We moved the upstream bugtracker to GitHub a long time ago. If this issue still affects you please re-create the issue here: https://github.com/hughsie/PackageKit/issues
Sorry for the impersonal message, and fingers crossed your issue no longer happens. Thanks.