Preheat the oven to 400 degrees F. Place red pepper, zucchini, yellow squash, and onion on a large baking sheet. Drizzle with olive oil and toss until vegetables are coated. Season with salt and pepper. Roast vegetables for 30-40 minutes, or until tender, stirring occasionally. Remove vegetables from oven and let cool to room temperature. Reduce oven temperature to 350 degrees F.
Grease an 8x8 square baking pan and set aside. In a medium bowl, combine roasted vegetables, black beans, cumin, chili powder, garlic, jalapeño, and cilantro. Stir and season with salt and pepper.
Spread 1/4 cup of enchilada sauce into the bottom of the baking pan. Add a layer of tortillas, to completely cover the bottom of the pan. You might have to cut the tortillas to make them fit. Top with 1/3 of the vegetable/bean mixture and 1/3 of the cheese. Make a second layer of tortilla, enchilada sauce, vegetables/beans, and cheese. Top with with a layer of tortillas, enchilada sauce, vegetables/beans, and cheese. Spray a sheet of aluminum foil with cooking spray and cover the pan.
Bake enchiladas for 20 minutes. Remove the foil and bake for another 10 minutes, or until cheese is melted and the enchiladas are bubbling. Remove enchiladas from the oven and let cool for 10 minutes. Cut into squares and serve warm.