The speculation is that the bones lose their density owing to lesser gravity. But scientists are not sure of the mechanism involved.
But I wonder,
1) Could it not be something lot simpler, and from the known territory of science, like absence of sunlight and hence absence of vitamin D?
2) Or does this happen inspite of the astronauts taking regular 'vitamin D' suppliments?
3) And anyways, even if they took all the supplements, who said science has discovered all the vitamins, and especially all the vitamins and substances human beings produce by 'photosynthesis' apart from Vitamin D?