Nice catch!  This issue is certainly related to the lack of management system for units on a tile.  This could be achieved relatively simply with a UI grid similar to the trade and inventory screens, with options to choose which unit is leading each army.

I tried to reproduce this in-game but it did not always happen.

What I had to do was follow these steps.

1. Create an army with a champion and a summoned creature. The champion leads it at this point.

2. Move in your sovereign to the army. SOMETIMES the game will display the order of units like this:

Note that this does not always occur - sometimes the order will be sovereign - champion - summoned creature.

3. Move your sovereign out of the stack. You end up with an army that looks like this:

Note how the champion is not leading the army any more.

Edit: I reproduced it using the same steps in an un-modded game. Can't be arsed to change the screencaps though.

Posted before

Sincerely
~ Kongdej

The specific bug encountered here is that an army with a champion would sometimes be unable to enter goodiehuts or quests. What you are describing is important, but a separate issue. Derek Paxton has commented that multiple armies on the same tile is one of the large things they'll likely be fixing after release.