I was playing a custom map with Islands and one of the factions was on a small island

I went to eliminate this faction and I captured the one city, but did not fight the sovereign so the faction was not killed.

The city covered the entire island and when faction sovereign and some other not in the capture battle (no idea whee they were) wound up in the city stacked with my guys. It became impossible to fight any of the faction survivors.

So try a case where a city covers an entire island