We've had the same problem for a while. I have an ongoing ticket where I dump new duplicate entries and Support merge them for me. I noticed that duplicate entries usually appear if there is a significant time difference between enrollment via Settings and Agent installation. It also happens sometimes when users install Agent first and enroll via Setting right away but almost never happens when they do the opposite. Another problem mentioned above is "zombie" enrollments when devices are stuck in "Synchronization is not yet complete" state and it is impossible to trace what they are. ... View more