Preheat oven to 350 degrees F.
In a medium bowl combine melted butter, sugars, and vanilla. Mix well.
Slowly stir in egg.
Add in pecan pieces, cinnamon, nutmeg, and chocolate chips. Stir to coat.
Place frozen phyllo cups onto a baking tray.
Add a teaspoon of batter into each phyllo cup.
Place baking tray with chocolate pecan bites into the oven for 10-15 minutes.
Remove chocolate pecan bites from the oven and let cool completely before serving.