A support case has been created to investigate this issue.
Ok, so after a few months of observing the workflow of the user that was having "ghost CUs" populate in their Design table of contents, we have identified this issue to be user generated. We were not able to generate the issue with other users, so we narrowed it down to the workflow of the user. The initial thought was that the issue occurred when running the WL to CU tool, however, after observing the user I noticed disassociated CUs prior to running the WL to CU tool. Realizing that there were already disassociated CUs prior to running the tool allowed me to narrow it down to what the user was doing when installing CUs in the design. I realized there were CUs being removed from the map however not deleted from the design. Also, found that CUs sent to the design yet not associated to an existing WL or created on the map it will populate as a disassociated CU in the Designer table of contents.
Thanks so much for monitoring this and tracking it down. Yes, the CU, or actually the feature associated with the CU will appear as disassociated if it is sent to the Design but not sketched. Once it is sketched it will have the asterisk symbol. So is this user going to change their workflow to prevent this in the future?