Were the flutes able to make a scale of some sort? That is, is there any indication that the people understood math?

There's no reason for a scale to involve any particular mathematics. Most flutes are made empirically, and the scale patterns used on them vary enormously - some are deliberately designed to not even play octaves, others play in a different scale from the singers and other instrumentalists in the same group at the same time. This even in quite technically sophisticated cultures. You can't conclude a thing from the natural scale of these flutes, even if you can work it out (which I am dubious about).