Yes, I think you must contact NetApp support . As the clone is deleted manually outside of SnapCenter, SC database (NSM) is not aware of the changes and it will continue to think that the clone exists. As the kb suggests - Please reach out to - NetApp support.
https://kb.netapp.com/Advice_and_Troubleshooting/Data_Protection_and_Security/SnapCenter/Unable_to_delete_SnapCenter_resource_group_due_to_backup_having_mounts
https://kb.netapp.com/Advice_and_Troubleshooting/Data_Protection_and_Security/SnapCenter/Failed_to_delete_clone_in_SnapCenter