Preheat the oven to 350F and line a 12-count cupcake pan.
Whisk together the hot water and ground flaxseed and set aside for 5 minutes. Sift together the flour, sugar, pumpkin pie spice, baking soda and salt in a large mixing bowl.
Whisk the flaxseed egg, pumpkin, banana, coconut oil, molasses and vanilla extract together until mostly smooth. Add the wet mixture to the dry and stir until there are no dry spots. Fold in the pecans and chocolate chips until combined.
Divide the dough between 12 cupcake liners, they will be slightly higher than the liners. Bake for 28-30 minutes or until an inserted toothpick draws clean. Place the muffins on a cooling rack and cool for 5-10 minutes before eating.