Preheat the oven to 400°F. Spray a 12-cup muffin tin with nonstick spray.
Spread the squash in a rimmed baking sheet, drizzle over the melted butter, and season with salt and pepper to taste. Roast the squash for about 20 minutes until tender and golden brown. Remove the squash and leave the oven on.
Meanwhile, in a medium saucepan, heat the oil over medium high heat. Add the garlic and sauté for 1 minute, until golden. Add the chili powder, cumin, and tomatoes, and bring to a simmer. Lower the heat to medium low and simmer for about 5 minutes. Let cool.
While the sauce is simmering, place the chicken in a large mixing bowl and add the black beans, scallions, jalapeno, and cilantro. Season with salt and pepper, and toss to combine.
Pour the cooled sauce over the chicken mixture and toss to combine. Gently toss in the roasted squash.
Heat a heavy pan, such as a cast iron pan, over medium high heat. Place a tortilla in the skillet, let heat for 20 seconds, flip, and heat for another 20 seconds. Transfer to a plate, and repeat until all of the tortillas have been heating, stacking them on the plate as you go. Cut the tortillas into quarters, and then take three triangles and fit them into a muffin tin so that they overlap, and cover the bottom and sides, and the round edges peek up just about the tops of the cup.
Place about ½ cup of the filling mixture into each cup. Sprinkle over the cheese, and bake the cups for about 20 minutes, until the cheese is melted, and everything is hot. Let sit in the tins for about 5 minutes, then remove and serve warm, with sour cream and salsa, if desired.