Heat oven to 375°F. Mist a 9×13-inch baking dish with cooking spray and set aside. Heat olive oil in a large sauté pan over medium-high heat. Add chopped onion, butternut squash, bell pepper, mushrooms and all the seasonings. Sauté for 6-9 minutes, or until softened and fragrant. Stir in the diced green chiles, chopped garlic, beans, corn, chicken and 2 cups enchilada sauce, stir well to combine. Remove from heat and set aside.
Pour about 1/2 cup of the remaining enchilada sauce in the baking dish, and spread until the bottom of the dish is evenly coated. Top with a layer of about 8 - 10 tortilla halves, so that the entire dish is covered evenly. Top with 1/3 of the chicken and veggie mixture. Sprinkle a layer of cheese.
Repeat with another layer of tortillas, chicken mixture, and cheese. If you still have enough left, add a final layer of tortillas, chicken mixture, the remaining 1/2 cup of sauce and cheese.
Cover the dish with tin foil. Bake for about 15 minutes, remove the aluminum foil and continue to bake uncovered until cheese is lightly browned and sauce is bubbling all around about 10 -15 minutes more. Remove from the oven, let it sit for a few minutes before cutting up into squares and serve warm. Add all toppings and garnish of choice before enjoying.