If there are two armies on the same square, and that square is attacked, I think the defender should have the ability to choose which army fights in defense.
My story: I began casting the Spell of Making when my sovereign was sitting in a border outpost. Unwise, but I hadn't read carefully, and didn't realize he'd be immobilized. So I parked a big army on that same square. Two turns before victory, an AI came in with two fast hero units, they each had 3 movement, and were able to run up to the outpost and attack, before I could spot them. No 'enemy units in your territory' warning. When tactical opened, I found that my sovereign had been pulled in to fight. So my big army had turned out to be useless. I lost. And that was that. But I feel like I should have been given a dialog box, where I could choose which army would fight the AI, the one that consisted solely of my sovereign, or the big bad army I'd build to defend him.
