Is this user a prexisting user in this org where the AD integration is done?
If so, if the user was manually created, it will not have the "External ID" set in the BMCServiceDesk__UniqueUserIDInSource__c field on user object.
It is the value in this field which "maps" a user on AD to Salesforce.
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In Salesforce, user’s record "BMCServiceDesk__UniqueUserIDInSource__c" (external id) field stores the active directory "userPrincipalName". If “External ID” is not populated, then here it is trying to insert the new user rather the updating the existing record and giving duplicate username error. You can correct the existing records using data loader. After correcting the data this will work.
If records are created through AD migration using Pentaho then it take care of this and populate "BMCServiceDesk__UniqueUserIDInSource__c" field then next run update the same record information and sync with Active directory example manager information.