I've seen this bug a few times when one of my melee ships takes a city. It will say the city is taken, and will kill the garrison unit, but the city remains in enemy control.
Sometimes if I reinvade it works, sometimes it will occur several times in a row. Eventually I will be able to take the city.
Sometimes if I reinvade it works, sometimes it will occur several times in a row. Eventually I will be able to take the city.