I don't know why nobody ever answered you, it seems the mods/admins are MIA. But I have played this mod a ton and never had any problems with clones. Are you using a mercenary function or something? This is known to be bugged code -- also in Perisno, etc. I suggest just not using whatever feature makes you join an army, iirc I saw something like "join as a samurai retainer"? is that it.. well don't do that.
edit: I just read your thread title lol-- yes -- Freelancer-- it's bugged, it's always been bugged it's bugged in several mods-- don't use it.