For the purposes of Access Control in a database duplicate groups will cause an issue and only one should exist.
It will not matter if you delete one of the duplicate groups so that you know which is the most recent and the group being used for permissions.
I have seen some applications that modify groups create duplicates on occasion or replication conflicts in multiple server environments.
If you have multiple servers try to get all address book modifying agents to run on a singe server.
On single server environments get agents that modify the address book to not overlap their running period if possible.
You can create an agent that periodically looks for duplicates and either removes the duplicate or tries to merger the members into one group or any other process you like to use.