If you mean a burned pin on the connector on the motor itself, then it could be a bad connection inside the motor. But it's more likely a bad crimp connection in the wire going into the connector.
If you mean a burned pin on the motor connector on the Duet, then it'a almost certainly a bad crimp connection on that pin. But check the underside of the Duet too to make sure that the pin is properly soldered into the PCB.