I think I found the issue. The Matriarch explodes if she reaches the house, but that doesn't count as "killing" her. This might happen if your build isn't strong enough, which would explain why you managed to kill her on a second run, probably with a stronger build, and got the achievement.
In any case, I'm adding a message to make this clearer. While I'm at it, I'm also separating Dr. Ferrán's dialogue to make it easier to follow.
Thanks for the feedback!