Shaaka: When you have liberated a cities, example Omerta or Drassen, enemies will from time to time tried to attack and take back the city you have controlled. Usually the enemies will move in patrol groups, higher difficulties tends to make the enemies attack in greater number, they will travel in standard patrol groups and depends on each difficulties will sometimes gather on the adjacent sectors to cities they intend to attack.
Actually it is a proven strategy that instead of being attacked in the city sectors, you send your merc to attack the enemy patrol in the city outskirts, hence it will not cause any casualties in your militia, and avoid any potential civilian casualties in the city sector (if you played the battle that is). Also you get to choose when to attack, whether on night attacks or day attacks. That being said if you destroy the enemy patrol group, if it is located near to any cities, said cities will gain some loyalty (if you win that is) or lose some (if you lose).
Another tip, every time you fully liberated a cities (freed all 3 sectors of Drassen) expect some counter attacks in said cities, that being said sometimes if you are unsure you can't hold a cities from counter attacks (many wounded mercs, little to no militia defending) you can choose not to liberate that last sector and instead recover and regroup, including training some militia in other sectors first, though if the cities had a mine in it, not fully liberated the cities means less income from the mine.
Thanks for the advice, everybody. I was very unsure of how this worked, and the manual is not very enlightening.