This bug is created as a clone of upstream ticket:
https://fedorahosted.org/freeipa/ticket/2258

Originated from ticket 1025.

From 389-ds FAQ:

If conflicts occur, the conflict resolution algorithm will resolve them, and if that is not possible, the conflicts are flagged for viewing by the administrator.

Each modification is assigned a Change State Number (CSN) which uniquely identifies the modification. Part of the CSN is a timestamp, and part is the identifier of the master on which the change originated. The conflict resolution algorithm usually processes the changes such that the "last one wins" based on the timestamp, but there are many corner cases which require special handling (for example, if an entry is removed from one master and at the same time a child entry is added to that entry on another master). 

To find conflict entries see the 389-ds documentation at:

http://docs.redhat.com/docs/en-US/Red_Hat_Directory_Server/8.2/html-single/Administration_Guide/index.html#Managing_Replication-Solving_Common_Replication_Conflicts