Not properly measuring ingredients
Recall that baking involves science. While you make the batter for the cupcakes, picture yourself in chemistry class. You undoubtedly recall how insistent your teacher was on exact measurements, forcing you to stoop to measure liquids at eye level and using scales to measure dry components precisely. A small measurement error like that might alter the flavor of your cupcakes, even though adding an extra sprinkle of salt to the batter won't likely have the same explosive consequences as it would in a chemical solution.
Sally's Baking Recipes, a baking site, offers advice on how to measure the ingredients for cupcakes. She suggests that flour be scooped out of the bag with a spoon into the measuring cup, leveled out evenly over the top, and never packed down. They also recommend exact amounts for granulated sugar, confectioners' sugar, baking soda, and cocoa powder. Brown sugar, in contrast to granulated sugar, needs to be firmly packed into the measuring cup. When measuring liquids, you should bend down to measure at eye level. When measuring butter for a recipe that calls for melted butter, you should do so while the butter is still solid.