This is the opposite issue, and would be much less of a concern. In this example, you are plugging in a connector that does not have any wires on the unused pins, and on the car side, you also would not have any voltages on the two unused pins.
The situation I described would be plugging in a hypothetical 3-phase EVSE into a car that had dummy pins on it. Once the EVSE switched power on, now you have two hot lines terminating in the inlet port. Perhaps this is not a huge electrical safety issue as long as there is suitable insulation protecting those unused pins from touching something, or perhaps even the EVSE could determine that the two extra phases were not in use and open independent contactors on the EVSE side for additional safety (for all I know, maybe they already do that in Europe for cars that don't support 3-phase charging).