I had this issue twice in a single early game just this morning.

I was exploring with 3 champions (sov, janusk, +1), and had an enemy come up to the far side of a city before I had time to build any protector units. In order to defend the city, I ordered the champ stack to attack the enemy (neutral) unit from the other side of the city. The stack entered the city, then left the city to the square I ordered, which resulted in the friendly stack, and the enemy unit (a darkling first time, and a bandit second time) followed up by destroying my city.

Very not fun to not initiate important combats when you need to. Especially since certain early game buildings cannot be rebuilt once destroyed (beacon of hope).