Preheat oven to 350 degrees F. Coat a mini muffin tin (or a regular muffin tin) with cooking spray or line with paper baking cups.
In a large bowl, stir butter, maple syrup, yogurts, egg, and apple, breaking up the butter with a spoon.
Sprinkle the flours, baking soda, baking powder, cinnamon, allspice, clove, and salt over the wet ingredients. Stir until just combined, being careful not to overmix (batter will be lumpy).
Divide the batter among the muffin cups. Bake until the tops of the muffins are lightly browned and a toothpick inserted into the center comes out clean (about 10-15 minutes for mini muffins or 20 minutes for larger muffins).
Turn the muffins out on a rack to cool.
Wrap tightly and freeze if you would like to keep these muffins on hand for quick breakfasts or snacks.