I have been using the same rolled sugar cookie recipe (No Fail Sugar Cookies) for years and sometimes air bubbles form when they are baked.

What causes them and how can I prevent them?

Do the air bubbles occur in the dough after you cut out your first batch and then roll out the second batch with the same dough? If so, make sure you knead it really well between rolling. This is a common occurrence and it is very hard to prevent this in subsequent rolling. If I get bubbles after baking, I take a small rolling pin (one used for detail fondant it is about 8 inches long) and gently rub over the top of the cookies immediately after I take them out of the oven. Actually, I do this even if there are no air bubbles, it gives the top of the cookies a very flat, even surface to decorate.

Do the air bubbles occur in the dough after you cut out your first batch and then roll out the second batch with the same dough? If so, make sure you knead it really well between rolling. This is a common occurrence and it is very hard to prevent this in subsequent rolling. If I get bubbles after baking, I take a small rolling pin (one used for detail fondant it is about 8 inches long) and gently rub over the top of the cookies immediately after I take them out of the oven. Actually, I do this even if there are no air bubbles, it gives the top of the cookies a very flat, even surface to decorate.

You will notice that the bubbles appear after the first cutting when you reknead the dough to do a second cutting. Air gets trapped between the layers as you reknead. I just use my spatula by pressing on the bubbles as soon as the cookies come out of the oven but are still on the cookie sheet to deflate the bubbles. Watch because they will reinflate sometimes. Just press gently and in a few seconds you will have nice flat cookies.

There are also techniques for kneading that will work the air bubbles out if your dough will stand up to extra kneading. I use a technique that I learned for wedging clay - it works like a charm.