If an auton gets the kill that triggers the loyalty change on zoanthropes, the ships will follow the auton rather than the player.

If the player then retrieves the auton, the zoanthropes then follow the auton into the auton bay and are instantly and permanently deleted.

...honestly not sure what the expected behaviour is here. We should probably have them latch onto the player rather than the autons as a general catch-all and to prevent them doing this.

I've attached a clip of this bug in action. The game is modded with Elemental Shift, but the bug isn't triggered by anything unique to the mod - this should happen if you can get a vanilla auton to pull it off.