After completing the optional mission to defend the three systems. The one that would award you with three leaders for each fleet? I was rewarded instead with -1 leaders for all three factions that stuck.
Now, if I loose a leader? I can never replace him. If I gain I leader? Jokes on me! I didn't. Had I known I was enabling hard mode with that mission. I wouldn't have attempted it.

If someone could tell me where the save file is, I'd like to edit these -1 values back 1 as my most recent saves is right before the mission ends in success. So I'll go in, finish the mission, then correct the bug.