I experienced the same core bug but there was no actual invasion of the town.  Enemy units where massed outside but I had stalled them with strategic spells.  When I moved my actual combat units outside of the city to attack, the militia stack joined in the attack.

After the combat I also saw the large militia unit on the strategic map and directed them back into the city where they disappeared.

To be fair, I have yet to reproduce this error after hundreds of hours of game-play. I'm sure when they find out where the error is happening it will get fixed.

Well, for this game I have kept the save file, but I don't know if it could be helpful.

Anyway I solved the problem by sending the guardian statue group to suicide against an enemy unit