Preheat oven to 350°F. Line or grease a 12-cup muffin tin.
In a large bowl, whisk together flour, baking soda, baking powder, salt, cinnamon, and nutmeg.
In a separate bowl, combine discard, melted butter, brown sugar, eggs, vanilla, and milk. Mix until smooth.
Add the wet mixture to the dry ingredients and stir just until combined — don’t overmix.
Gently fold in chopped apples.
Fill the muffin pan ¾ of the way up with muffin batter.
Next make the crumb topping by combining flour, brown sugar, cinnamon, and salt. Add the cold butter and cut it into the dry ingredients with a pastry cutter or fork until the mixture becomes crumbly. Sprinkle the crumble on top of the muffin dough.
Bake for 20–25 minutes, or until a toothpick comes out clean.
Let cool in the pan for 5 minutes, then transfer to a rack to cool completely.