I was thinking the same as I played through. *Spoilers ahead for anyone reading who hasn't played the game.*
I'm thinking it was the wolves eating them? 'Cause I kept a head count every day when I turned in, and I kept losing more and more. I don't know what else it could have been. In the moment, their disappearance was terrifying, but in hindsight, whatever it was, it adds to the depth of struggle and failure that Stillness' gameplay forces you into. Probably my favorite thing about it.