I'm seeing this in the scenario, but I'm not sure it's a scenario-only problem, since I think I've seen it before.

I have just captured the Magnar city of Khaffara, defeating an army of 18 defenders.  After the battle, my army appears to be standing on top of the city, instead of inside it:

If I select the city, I see that Relias and all but one member of his army are in the city:

However, if I select the army standing on the city, it is labelled Jordur the Giant's army (Jordur was the one unit missing from Relias's army in the city) and it contains all of the same units from Relias's original army except Relias.

After saving and restoring, I still see the same thing, so here's the save if you need it.

Selecting and moving the army on top of the city works.  Selecting all units inside the city and attempting to move them out of the city results in only Relias moving out, and the city then appears empty.  So it looks like all of the units that were shown inside the city except Relias were phantoms.