In build 12.0.5000 (SQL 2014 SP2) I attempted to use the new DBCC CLONEDATABASE command on an existing database. I got the following error:
Msg 2601, Level 14, State 1, Line 1
Cannot insert duplicate key row in object 'sys.sysowners' with unique index 'nc1'. The duplicate key value is (<username>).
where <username> is one of the users in the database I chose for cloning.
Other databases on the same instance clone fine.
So it looks like for some reason it is trying to insert the row for this user twice into the clone.
Incidentally I ran a DBCC CHECKDB on the db it's failing to clone and that reported no errors.