I didn't have a save game before what happened, so I'll list the steps from memory.
- I walked my little sovereign army into the territory of Ilyana, declaring war on him quite a few turns after starting research and trade treaties.
- The sovereign was standing outside his only city.
- A caravan was one or two move away from the city.
- I attached the city, killing the sovereign's lady friend (not sure if it was a bride or just an ally) and took over the city.
- The moment the battle was resolved, the screens transitioned quickly, and a caravan arrived from what was now my city.
- Problem: From this moment on, I wasn't able to select by click, select by tab, select by shift-u... I was no longer able to select the army in the city. It was as if my army had disappeared.
I quit out of the game, and luckily had an autosave on the same turn that I took over the city. As soon as I find a place to upload the file to, I will. There is also a screenshot showing the city that is clearly under my allegience, but incorrectly (or perhaps correctly as far as the game is concerned 
) displayed as a caravan.
Short term workaround:
I reloaded the game and I realized that at the very beginning of the reload, my army was accessible. I could move them out of the city, and then back in, and the city was fine from there. No more confusion with the caravan.
To reproduce the bug from my save game:
When you load up the save game, which I need to upload first to... someplace... make sure to click on the city directly. Do not try to move the army from the city. Clicking on the city directly will bring up the odd Caravan reference, and lose access to the army.
