Preheat the oven to 375 F.
Make the crumble topping: In a small bowl, stir together the oats, flour, sugar, and cinnamon. Add the melted butter and stir to combine. Set aside. In a large mixing bowl, whisk together the flour, oats, sugar, baking soda, baking powder, spices, and salt.
In a small bowl, whisk together the eggs, applesauce, and yogurt. Fold in the melted and cooled butter and stir well. Fold in the carrots, raisins, and pecans.
Scoop batter into 12 paper-lined muffin tins, filling each almost to the top. Spoon crumble mixture on top.
Bake for 25-27 minutes, or until muffins are golden brown around the edges and feel firm to the touch, even in the center. Let cool in the tin for 10 minutes. Bake off remaining muffins. Store covered at room temperature for up to 2 days.