I finally found the perfect solution for when this happens... for whatever reason... I find myself dealing with this more often than I would like to admit... and always with my chocolate cupcakes as that batter is a bit thinner than others... you would think I would have figured it out by now, but sometimes I just get in too big of a hurry.
While this may not always be an acceptable solution... most of the time it will...
First.... invert the cupcake onto a clean surface... I find it's best to let the cupcakes cool somewhat, but not get all the way to room temperature. Then get a circle cutter that is the same diameter of the top of your cupcake...
Press down until you've removed all the excess crunchiness... I find it's best to push the cupcake through the cutter.... top first, instead of pulling the cutter away from the cupcake....
Now you have a cupcake that's ready for decorating:)
Of course, there are those occasions where this may not do.... it may depend on the design going onto the cupcake... sometimes we like a little "edge" peaking out so our clients can see the yummy flavor of the cupcake. In that instance, a clean/baked edge is necessary.... or sometimes the presentation must be near perfection... for wedding perhaps... in those instances, it's probably best to save these for your kiddos, family and friends and start over.
These cupcakes, fortunately, are for my son's class at school. I think the fix is going to work just fine and I don't have to present giant "mushroom-like" cupcakes to his class.
Hope you found this tip helpful... I only just discovered it and I can tell you, I have chunked many a cupcake because of overfill!