Heat oven to 425°F.
Combine squash, onion, garlic, olive oil, cayenne, salt, and pepper in a large bowl. Toss until well coated with oil and spice. Spread in a single layer on a baking sheet.
Roast vegetables until golden and tender, about 20-30 minutes, turning halfway through. While vegetables are roasting, wrap tortillas in foil and warm them in the oven, about 10 minutes.
Pour vegetables back into a large bowl, add black beans and coarsely mash with a potato masher. They don't need to be smooth, just broken up a little bit. Stir in half the cheese.
Pour enough enchilada sauce on the bottom of a 9 x 13-inch baking dish to cover. Lay one tortilla on a work surface and place about 3 tablespoons of filling in the middle. Roll the bottom up over the filling and continue rolling to close. Place seam side down in the baking dish. Repeat with the remaining tortillas and filling.
Cover enchiladas with remaining sauce and sprinkle the remaining cheese on top. Return dish to oven and bake until sauce is bubbly and cheese has melted, about 20 minutes.