Hi there; I think that's not a bug and works as intended, just wanted to post it here, maybe you can change that in the future. So when you activate the startup setting that Zombies are in the "enemy" force and not in the "zombie" force (so that they don't kill off Biters), when you do that in an already running save, only newly spawned Zombie spawners have that "enemy" force, the already existing ones keep their "zombie" force. I stimbled upon this when running into strange behaviour in ERM, see here for reference https://mods.factorio.com/mod/enemyracemanager/discussion/691dbe2aadf0ace748c4f612.

Maybe you can update existing Zombie spawners to have the "enemy" force if this setting is turned on later in a game, though I don't know if that's difficult or possible at all, I think what I encountered is pretty much an edge case and not many other players will face this.