This question is an exact duplicate of:
In two sets of Sha"S Bavli that I own, and logically, Rosh HaShanah precedes Yoma. But it doesn't in the Daf Yomi cycle. Why not?
My first thought was that, perhaps, my sets deviate from the traditional order. So I checked, and sure enough, in two sets of Mishayoth that I own, the order is the same as the Daf Yomi.
But then I checked a set of Sha"S Yerushalmi, and, although it's close to the Mishnah's order, it's not identical (Beitzah and Rosh HaShanah are out of the Mishnah's order, yet Rosh HaShanah does not precede Yoma).
So it seems that Daf Yomi follows the order of the Mishnah even though neither Sha"S Bavli, nor Yerushalmi, follows that order.
So again, my question: Why?