I did the quest that gave me the Panca archers. Since I already had a full army of troops, the Panca archers stacked with my army. When I selected the archers and moved them away, my army stack was shown on the map as only my sovereign with no other troops:
As you can see from the bottom part of the screen, she's not alone.
Not surprisingly, saving and quitting the game at this point and then reloading the saved game doesn't show the problem, she's shown with accompanying troops.