Preheat oven to 400 degrees F. Coat a 12-cup muffin pan with cooking spray.
In a medium bowl, whisk together the all-purpose and whole-wheat flours, baking soda, salt, cinnamon, ginger, cloves, and nutmeg.
In a large bowl, whisk the sugar, molasses, oil and 1 egg until combined. Add the other egg and whisk well. Whisk in the pumpkin and vanilla. Whisk in the flour mixture in 2 batches, alternating with the buttermilk. Whisk just until combined.
Pour the batter into the prepared muffin pan and sprinkle with the pumpkin seeds. Tap the pan on the counter a few times to remove any air bubbles. Bake for 20 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. Run a knife around the muffins to loosen them and unmold. Cool completely on the rack.