Saute the onion in a medium-sized saucepan until it begins to soften. Add the garlic and cook for another minute. Stir in the bell pepper and squash and cook, stirring, for about two minutes, until squash is just beginning to become tender. Add the cumin, chile powders, black beans, and salt. Simmer for 5 minutes. Remove from heat and stir in the nutritional yeast and lime juice. Check seasoning and adjust to taste.
Preheat oven to 350. Lightly spray one large rectangular baking dish or 4 individual baking dishes with olive oil. Place a thin layer of enchilada sauce on the bottom of each dish, reserving most of it to go on top. Microwave the tortillas for about 20 seconds to soften them. Place a tortilla in front of you and arrange about 1/4 cup of the bean mixture across the center. Roll up and place seam-side down into the baking dish. Repeat with remaining tortillas and beans. Pour the remaining sauce over the top.
Bake for about 20 minutes, or until hot and bubbling. Sprinkle with sliced green onions to serve.