I would not be unduly upset. It has happened to me. I have had chicks fail to thrive, and die in a day or so, but not often, but not rarely, I have lost a bird at about 3 months that seems to be fine with healthy flock mates, to be found dead. All the rest of the birds seem fine and go on to live normal chicken lives.
I would not do a necropsy unless, you lose some more, or if others get sick acting. I think it is a genetic issue and as they get bigger, they outgrow the internal physical defect.
Mrs K