If you want Apper to only notify you about official patches edit the file /etc/PackageKit/ZYpp.conf to say:
Not doing so results in new updates being announced by Apper far too often. Mostly, the updates contain minor application updates.
In my opinion, the user should only be bothered with important security updates.
(Alternatively, the application updates could be grouped together to packages of a certain size. So that not every day one or two new minor updates are presented to the user.)
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.