Preheat oven to 375°F. Lightly grease a 9x13-inch baking dish.
In a large skillet, heat olive oil over medium heat. Add diced onion and cook until softened, about 2-3 minutes.
Add cubed butternut squash, minced garlic, chipotle chili powder, cumin, salt, and black pepper to the skillet. Cook until squash is tender but still firm, about 6-8 minutes. Stir in black beans to warm, then remove from heat.
Spread a small amount of enchilada sauce on the bottom of the prepared baking dish.
Spoon a heaping 1/2 cup of the squash and bean mixture onto each tortilla, roll up tightly, and place the seam side down in the dish.
Pour remaining enchilada sauce over the rolled tortillas and sprinkle with grated cheese.
Bake in the preheated oven for 20-25 minutes until the cheese is melted and bubbly.
Allow to cool for a few minutes before serving.