The "invisible unit" joining ones army are copies of Marnid... It happens exclusively with Marnid. The correlation seems to be one Marnid per battle, but I am unsure of this, it's possible that its 1 per Marnid KO. Perhaps it's "reviving" him when he never died, resulting in two Marnids... I do not believe it has to do with being an Aid (speaking of aid, I have Ymira as one... Her skills show up on the skill list properly, does that signify that I am getting the benefit from them (I.E. First Aid?)). I set Marnid as an aid at one point, but he was not an aid when I received duplicate soldiers to my knowledge. I have 12 copies of Marnid... I can get rid of them by telling him to seperate from me (wait here). In which case there will be 12 copies of marnid sitting on the same tile (or 12 on different tiles if you move each time before telling him to wait here). This has not reproduced itself with any other NPC in the party, only Marnid. I had just won my first castle (a nord castle) and noticed I had 15 soldiers in my army when I actually only had myself, Rolf, Ymira and Marnid. So I told them all to wait seeing if I counted as 12 soldiers for some reason, and Marnid could repeatedly be told to wait, 12 times, each leaving a copy on the world map. When I bump into him, one copy will rejoin (making 1 in the party) but if a pre-existing Marnid is in the party, it will give me the choice of forcing him to surrender or die. Choosing that results in Clone Marnid calling me a dirty scoundrel. When choosing to "charge the enemy" (at least on the screen) the only option is "leave." Doing this serves no purpose as Clone Marnid still occupies the spot.
I believe I have a theoretical solution to this:
Do not recruit Marnid
Until a fix is made, I would suggest all players of this mod to ignore Marnid or get many copies of him. The copies will either litter the world (unless you neatly stack EVERY copy on the same little area) or fill up your army with Marnids. Even though he only registers as one unit (only one appears in combat and shows on the list in party).
Edit: Absolutely amazing Mod, by the way. Native should have had a way to make your own faction. You corrected this. Kudos.