Hello Manny,
That is most unfortunate, for the process has worked many times for me in the past.
In answer to your question; No, for the process to stage the update through the Patch Remediation Center creates the necessary resource associations in the database in regards to the targeting IsApplicable & IsInstalled Rules of the update.
The steps to disable the bulletin in the PRC, delete the physical packages and delete the Resource Associations (as detailed on the KM) should resolve this issue once only the recent APSB13-11 is staged.
Additionally, it may be an outdated PMImport failing to show the modified date of the update in the PRC.
You may want to open a support case to have the Patch Support Team review the issue and find the cause of the anomaly if none of these steps resolve the issue.
Thank you,
Joshua