Hard to say without seeing your recipe or knowing how you're rolling out your dough. Do you dust your work surface with anything? If so, what? Do you get bubbles on the top of all cookies, i.e., even those on first roll, or just those on later rolls (if re-using previously rolled dough)? Sometimes I get a few bubbles on second and third rolls, because working the dough activates the gluten in it, and any trapped air between folds of dough can lead to bubbles when that air heats up and expands in the oven. Also, rolling out with confectioner's sugar can do weird things to the cookie surface - cracking, crinkling, etc.