Currently an error is thrown when trying to merge two constituents who are registered for the same event. As a result, there are many records in the database that cannot be merged. Ideally there would be some type of merge processing that could occur to allow the records to merge, even if the target constituent doesn't result in multiple registrations for the event. Idea bank issue http://bbecfeedback.uservoice.com/forums/23106-crm-feedback/suggestions/7664364-allow-a-constituent-to-register-for-the-same-event is related and will provide some context.