When you import camt.054 where Payment reference on the file is on the Ntry level and the Ntry includes more than one TxDtls (payment transaction(s)), the payments are imported with the same payment reference and warning is thrown:
Transaction with reference xxx is already imported with voucher yyy
It would be rather expected that payments are imported with the same payment reference without warnings and the control should take place only, if the reference is found in other payments journals, not in the one the import takes place