Having just started a new game, the first city was built next to some enemies. When the enemies attack the city, the Sovereign is listed as the only defender; the two other starting units stationed in the city, as well as the militia, are not included in combat (resulting in game-over, since the starting level hero can't defeat the enemies). Consistently happens with the following savegame; sometimes takes a turn or two for the darklings to attack.
https://dl.dropboxusercontent.com/u/89188843/missing-city-defenders.EleSav