I've played for a couple weeks. Never used Rally Points before until now. I'm in the Mine Enemy mission. Trying to open the door where you have to step on two pressure plates. Presumably your Bridge Officer steps on one plate you step on the other and the way to accomplish this is by giving your BOff a rally point on the pressure plate. Clicking the Rally Point icon on the BOff's interface gives you a new mouse pointer. Left clicking on the ground anywhere to "place the rally point" does nothing. The BOff never moves no matter where you click the rally point mouse pointer.
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https://youtu.be/qwEU0UOad-o
https://sto.gamepedia.com/BOFF:_Set_rally_point
Not sure if that helps? My understanding there is that it's not left click itself, but rather a reference to "ContextAction 1".