Preheat oven to 350°F. Line a muffin pan with cupcake liners or coat with cooking spray.
In a small bowl, whisk together the 2 Tablespoons of ground flaxseed with the 6 Tablespoons of water and let sit while you start preparing the other ingredients.
In a small bowl, mix together the topping - 2 Tablespoons of sugar with 1 teaspoon cinnamon.
In a medium bowl, whisk together the flour, baking soda, baking powder, cinnamon and salt.
In a large bowl, mix the ¾ cup sugar with the softened butter until combined. Add the flaxseed/water mixture, pumpkin and vanilla. Stir in yogurt.
Fold the flour mixture into the wet mixture. Gently stir in the apple chunks.
Pour the batter into the prepared muffin pan and sprinkle with the brown sugar topping. Bake for 25 to 30 minutes or until a wooden pick inserted in center of 1 of the muffins comes out clean.
Let cool on a wire rack for 15 minutes.
Store any leftover muffins in the refrigerator for up to 3-4 days or up to 3 months in the freezer.