Preheat the oven to 400 degrees F.
Place the butternut squash cubes on a large baking sheet and drizzle with 1/2 tablespoon of the olive oil. Toss until well coated. Season with salt and pepper. Roast for 20 to 30 minutes or until tender. Remove from the oven and set aside.
While the squash is roasting, heat the remaining 1 tablespoon of olive oil in a large skillet over medium high heat. Add the onion and red pepper and cook until tender, about 5 minutes, stirring occasionally. Add the garlic and cook for one more minute.
Stir in the in the cilantro, cumin, chili powder, smoked paprika, and season with salt and pepper. When squash is done cooking, stir in the black beans and butternut squash.
Spray a 9×13-inch baking dish with nonstick cooking spray.
To assemble the enchiladas, Spread about 1/4 cup of the enchilada sauce onto the bottom of the greased baking dish.
Wrap the tortillas in damp paper towels and microwave on high for 30-seconds and then flip and heat for 30 more seconds. OR you can briefly fry the tortillas in hot oil. This will prevent them for tearing.
Spoon about 1/4 cup of the filling in the center of a tortilla. Add a tablespoon of enchilada sauce and a sprinkle of the shredded cheese. Roll each tortilla and place seam side down into the baking dish. Continue the process until filling is gone. It should make 12 enchiladas; but could vary depending on the size of your tortillas.
Pour remaining sauce over the top of the filled enchiladas and then sprinkle with remaining shredded cheese, there should be about 1 cup of cheese left for the top.
Bake for about 25 to 30 minutes or until cheese is melted and enchiladas are bubbly. Remove the pan from the oven and allow enchiladas to cool for 5 minutes. Garnish with cilantro, avocado, jalapeno slices, and queso fresco, if desired. Serve warm.