Are you seeing the duplicates only in Outlook? If you check that same message in webmail you see only the one copy?
As Douglas noted, any sync protocol aside from POP is maintaining an index of what is on the server. So, duplicates seen in that client's index can usually be cleaned up by resyncing that client (removing the account and/or profile, and removing the sync key from Settings>Connectivity>Synchronized Devices if using MAPI/EAS/EWS) and allowing it to pull down a fresh copy of the mail data from the server.
I do recommend completing that resync on the latest available public version though to ensure you have all of our latest fixes and improvements available when the resync begins.
Kyle Kerst
IT Coordinator
SmarterTools Inc.
www.smartertools.com