This is some kind of a case bug
.
Most cases have them split.
You can play with the connector though taking the metal clips out of the plastic thing.So if you have on the other connections (buzzer,Sw) split mini connectors you can switch between them easily .By using a needle you can dismantle them.
You could also try putting the connector in all possible positions between the 2 pins.Maybe the middle one is connected to one of the 2 needed ,who knows.An ohm-meter could check that.
By connecting it no harm should happen as it s a LED ,so try and see.
Never encountered the problem personally.Some cases even have a case LED connected directly to the PSU.
Otherwise let it be ,less annoying light if the PC stays up during the night.