Uh-oh. Sounds like one of two things happened: 1.) Your leavening (baking soda and/or baking powder) is expired, ~or~ 2.) You let your muffin batter sit for too long before baking. Here's the science behind that: This healthy muffin recipe calls for two types of leavening, both baking soda and baking powder. Baking powder becomes activated as soon as you add it to liquid. This means that as soon as you mix the wet and dry ingredients, it starts working. If you wait too long to put your muffins in the oven, the reaction from the baking powder will complete before the heat of the oven can solidify the batter around the pockets of CO2 that the leavening creates, leaving them flat and possibly a bit dense.