Preheat oven to 375 degrees. Lightly coat a 9x13 baking dish with cooking spray.
Warm olive oil in a sauté pan over medium heat. Add red onion, red bell pepper, cilantro and jalapeño pepper, and cook for 5 minutes.
Chop the banana squash into small chunks. Add the black beans and squash to the skillet. Stir to combine, then remove from heat and place in a large bowl.
Meanwhile, make the enchilada sauce by combining all sauce ingredients in a food processor. Pulse until smooth. Spoon 1/3 of the mixture into the baking dish.
Add 1/2 of the shredded cheese to the veggie bowl, and stir to combine evenly.
Place a few spoonfuls of the veggie mixture onto one half of a tortilla. Add a spoonful of enchilada sauce (use about 1/2 of what's left), then roll the tortilla up. Place in the baking dish with the open side down. Repeat with the rest of the tortillas.
Spoon the remaining enchilada sauce on top of the tortillas and around the baking dish. Sprinkle the remaining cheese on top of the tortillas.
Cover the dish with foil, and bake for about 30 minutes, or until the cheese is melted and lightly browned.