If you click on multiple RPM packages in a browser (on F11 beta) to initiate installation before the first installation has finished, so that subsequent installations show "Waiting in queue", when the queued transactions start, they will try to re-install the first package all over again.
For example, click on packages A, B and C, accept the security questions etc. While package A is installing, B and C will be waiting in the queue. After package A finishes installing, B and C will try to start in turn, but will each actually try to re-install A, resulting in an error that A is already installed.
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.