When the Mail Source Agent (MSA) is installed on a cluster and the active node changes (the cluster fails over), the licenses for the synchronized mailboxes on that cluster are counted a second time. Therefore, the number of used licenses is higher than it should be.
This is due to the fact that the mailbox licenses are stored by servername, rather than virtual servername. This is the exact explanation from product development:
Licensing information is stored within the registry key on the active node and only tracked by the node name and not by Exchange Virtual Server's name (EVS). Therefore, when on the one node there are two virtual servers running or cyclic change of nodes occurs the licensing information will be erased and rewritten with the new values from another node and new nodes name. This will be replicated to the license server and increase the number of used licenses for the same mailboxes.
CR39993 was created for this issue.
This situation will also happen if the Alternate Host is used as a replacement of the cluster. Please see solution SOL60678 - Alternate Hosts and correct procedure when introducing this feature in the middle of migration - https://support.quest.com/Search/SolutionDetail.aspx?id=SOL60678 for information on the Alternate Host feature. The situation is also likely to occur if the server hosting the mail source agent is changed from one agent host server to another or if a mailbox is removed from its original mail collection and added to a collection which uses a different mail source agent.
Please confirm that the licenses were used incorrectly. See the section on the Registry in solution SOL25143 - How to determine how many mailbox licenses are used? -https://support.quest.com/SUPPORT/index?page=solution&id=SOL25143 which will identify the licenses used by each server.
Please contact your Account Manager to obtain additional licenses.
Please note: In Migration Manager for Exchange 8.12 license counting mechanism has been changed and the issue will not occur any more for mailboxes migrated with this version.