Yes, that happens to me. What I can report is that during the raid, settlers will be "downed", and I can "execute" them, which seems to work fine. That is, when I turn on execute, they will sometimes rise up and require one more pop from my gun to kill, or sometimes die instantly. I don't know if that's normal or not, since this is the only time I used the execute function. Anyway, the execute option is available during the entire raid, and as the raid finishes (the secondary subdue finishes), I've seen a split second where a settler/civilian offers the "enslave" option instead of the "execute" option, and then an instant later they all die, with the exception of various essential npcs, it seems, like some of the NPCs at Warwick and Somerville, who then become slaves at that vassal. I never see an explosion, just a mass death.
I know we're trying to stay off the mass death part, just wanted to give the full picture of events.