I'm no expert; however, how much leavening are you using (baking powder or soda?) You might try reducing or eliminating that. Also, eggs can make dough rise and bubble (I believe.) If you beat too much air into eggs before adding them to your dough, maybe that might be giving your cookies bubbles. (For cookie recipes using eggs that I often make, I do fork-beat the eggs and add my flavor extract to that before introducing it to the sugar/butter mixture ...but I do it first thing and set it aside so it has time to fall back down a little, while still being combined well with the extract.)
This is simply my overall theory on the matter, though: cookies were developed to begin with when bakers needed to test the temperature of their ovens (pre-electricity days)--so they put a little batter in the oven first to make sure their cakes wouldn't burn or would cook. Cake batters, of course, need to rise and bubble upon baking to give them their light, fluffy texture--so the ingredients in the cake batters were developed to do that. But, cookies recipes were developed from those early days of baking cakes. If you want flat, dense(r) cookies, however, using cake ingredients that were designed to make them rise (eggs, leavening powders) actually counter that desired texture of thicker, more structurally dense cookies.
So, here is what I think, if you are having trouble with bubbling cookie tops: leave out or greatly reduce the eggs and baking powders/sodas. Maybe try a shortbread-type dough (butter, sugar, flour, salt, vanilla--that's it. Ina Garten has a delicious one that you could google. I get raves for cookies I make using that recipe, and I doubt you could make it bubble if you tried! LOL)
Good luck...again, I'm no expert--just someone who has been baking for more than forty years, so I've probably experienced every disaster that is known to bakers at one time or another!) [Also, never underestimate how your method of making doughs and batters matters...there is a reason one can't just dump all the ingredients into a bowl at once and stir--another lesson I've learned over the years! That's a whole 'nuther reason something could go wrong with a final product...]