Recently I noticed that several abilities deactivate the swarm ability on the s31 battlecruiser. I still dont know why basic bridge officer abilities do that. Today it got even weirder because for some easy battles I didnt even activate them. But then in the heavy combat I did and then I noticed the swarm is deactivated. Or so it looked like it. See:
As it turned out, it was inactive because no close range enemies were shot by the swarm nor was any audible firing present from the swarm. But the button still indicated otherwise.