It is possible to have several categories contain the same OU when you either run an offline mirror and the GPO is linked to multiple OUs, or during custom category configuration. However, if you are cleaning up GPOs or Merging GPOs and no longer need that GPO, you then have to track down every Category where that GPO exists in order to delete them before it will be completely removed from the Repository. GPA should offer the ability to either bulk delete based on search results and or offer an option to delete gpo from all categories.
The GPA 6.9.2 client has been extended allows the user to see all of the current "Category Links" for a GPO and take action on the "Category Links" that they have permissions for. Thank you for the idea.