In the updates view window, packages are grouped based on their main package name (if I know correctly, they are grouped based on their source rpm name). I think it would be very useful if the main packagekit window does the same grouping for packages which will reduce the clutter in the main window.
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.