Preheat oven to 400°F. Coat a muffin pan with cooking spray.
In a small bowl, mix together 2 tablespoons of the brown sugar, the pecans, and 1/2 teaspoon of the cinnamon.
In a medium bowl, whisk together the flours, baking soda, remaining cinnamon, and salt.
In a large bowl, whisk the remaining sugar with the oil until combined. Add the eggs, 1 at a time, whisking well after each addition; then, whisk in the applesauce and vanilla.
Add the flour mixture to the wet ingredients in 2 batches, alternating with the buttermilk and stirring after each addition just until combined.
Core, peel, and dice 1 apple; gently fold into batter.
Pour the batter into the prepared muffin pan and sprinkle with the pecan mixture. Tap the pan on the counter a few times to remove any air bubbles. Bake for 20 minutes or until a toothpick inserted in center of 1 of the muffins comes out clean.
Let cool on a wire rack for 15 minutes, then remove from the pan.
Cool completely before serving. Serve with remaining apples on the side.