This is due to how Luminate processes transactions and registers participants.

The registration processes the credit card first and foremost, before it will process registrations.  
If there is a Primary registrant, followed by two secondary registrants, the primary is not registered for the event, but it turns out the secondary are already registered, the system will create the primary registration, but will deny the secondary as they already existed.  The card will still be charged for the three registrations however, as that is the first part of the process, regardless of the outcome of the registrations.