Line mini muffin pan with 12 paper liners, set aside.
Melt chocolate chips and coconut oil in microwave for 15 seconds at a time, about 1 minute total, stirring in between until chips have completely melted. (You can also melt in a small saucepan on stove over low heat, or a double boiler. Just be careful not to burn your chips whichever method you prefer!)
Scoop about 1/2 tablespoon of melted chocolate into 12 muffin liners. (Scoop a little less and you should get about 16 cups.) Transfer pan to freezer and allow chocolate to set for 5 minutes.
While bottom chocolate layer sets, make your filling: In a small bowl, microwave coconut butter until slightly melted, about 15-20 seconds. Stir in pumpkin spice, pumpkin puree, and molasses or maple syrup until mixture is smooth. Set aside.
Take muffin pan out of freezer. Using 1/2 teaspoon, scoop a rounded ball of the pumpkin coconut butter (equal to about 1 tsp) and place on solid chocolate. Gently press butter down a little bit with back of teaspoon to flatten. Cover in more melted chocolate, about another 1/2 tablespoon. Transfer pan back to freezer for another 5 minutes until set.
I like to store my chocolate cups in the fridge, then allow to come to room temperature before eating. Enjoy!