При регистрации плагина выбираете Execution mode - Synchronous (Синхронный режим выполнения) - дубликатов быть не должно.
Цитата:
Synchronous and asynchronous execution of plug-ins. Synchronous plug-ins are executed in a pre-defined order as part of the main Microsoft Dynamics CRM event processing. Asynchronous plug-ins are queued and executed independently.