We went to the bakers at King Arthur Flour’s test kitchen for their thoughts on this question. Their response is, "We have two suggestions. The first is just as she suspects, she may need to get the "bubbles" out of the batter. If the batter is on the stiff side, just tapping it on the counter may not do the trick. One of the test kitchen crew suggested holding the pan at waist level and dropping it on the floor! (Not advisable if she is using a glass pan.)
"Another method might be running a spatula under some cold water then pressing down gently on the top of the batter, or running a knife through the batter in a swirling motion. The second thought here was that perhaps there is too much leavening in the recipe. But if it is a recipe that she has been using for a while and is just now noticing the craters, that is probably not the case."