This will help keep your pizza from getting big air bubbles while baking. (butterforall.com)
Cooking the flour in the saucepan cooks out the raw flour flavor, and begins to dry the dough out, so that one big air bubble forms instead of lots of little ones. (theredheadbaker.com)
It could be that the batter is undermixed so you're getting big air bubbles, or they could be puffing up too quickly in the oven and don't have enough structural integrity - a cooler oven might help. (pizzarossa.me)