I have the same issue, the dbua refuses to do the upgrade because it sees records in sys.recyclebin$. And I cannot get rid of them via the purge dba_recyclebin or other purge commands. The objects don't show up in dba_recyclebin. I am upgrading from 220.127.116.11 to 12.1.0. The objects could be objects created by oracle for XMLTYPE columns and object relational storage, but I am not sure.
I don't have the right with my support contract to create technical SR. I will try the manual upgrade procedure but on production I think it is not a good idea, so I hope in the mean time there will be a patch..