After upgrading a customer to vCenter to 6.0, VMs that were being replicated with Veeam from one site to another started to issue an alarm for a "VM MAC Conflict". However, when I compared the MACs of the replicated VM and the original VM, they were unique. I had not upgraded the hosts at this point, only vCenter. Nothing had changed with Veeam, so this was a new issue as a result of the vCenter upgrade.
As it turns out, there is nothing wrong technically, this is simply a change in behavior in the alarm issued by vCenter. When Veeam replicates a VM, the replica VM initially has all the same settings (other than the name) of the source VM. vCenter sees the same MAC address on two VMs and alarms. vCenter then changes the MAC address of the replica (as had always been the behavior), but it never clears the alarm. You must clear it manually. Then when the next replication occurs, the alarm will trigger again.
I found several references to this issue online and most had suggested simply disabling the alarm to avoid vCenter showing the replicas with an alarm all the time, but that's not a great solution because no alarm would be generated in the event of an actual MAC conflict. Further research revealed a workaround. You can edit the alarm VM MAC Conflict in vCenter and add an argument to exclude VMs whose name ends in "_replica".