Would it be possible to have countries which are poor (think Africa) or broken down due to the invasion be victim to terror scenarios involving insurgent militias. In these cases, we'd have to fight humans.
Perhaps we could have groups not unlike the Cult Of Sirius in Apocalypse. Such groups could arise through a Stockholm Syndrome type response to aliens taking control of their country. The aliens could be intentionally facilitating such a response through deception and promises of mercy . The aliens could therefore be more intelligent and manipulative waging psychological warfare, instead of just attacking everyone at random. So these human groups would be either "useful idiots" aiding the aliens and h ostile to X Com, or militias / pirates trying to make the most of the chaos.