[Sinapus]

It's an old problem. Colony modules have 200kt structure and mine warhead I do only 100 damage. Since mine attacks are run as separate combats, the colony module never gets destroyed. Or something like that. Essentially, you end up with a colony ship with everything, or almost everything except the colony module destroyed.

The temporary fix is to either lower the structure of colony modules to 100 kt, or change the research files a bit so the AI always researches Explosive Warheads 3 before they get ahold of Mines lvl 1.