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Preheat oven to 350 degrees F. Spray 9x13 inch baking pan with nonstick cooking spray.
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Make the sauce: Add tomato sauce, chipotle peppers with adobo sauce, greek yogurt, chili powder and garlic to bowl of a food processor; process a few times until smooth. Place in the fridge to thicken it up.
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Heat olive oil over medium heat in large skillet. Add garlic and diced onions and saute until garlic becomes fragrant (about 1 min).
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Add cubed butternut squash, stir, and cover for about 8 minutes or until fork tender, stirring occasionally to ensure squash doesn't burn. Add a few teaspoons of water to the pan if necessary to help the squash cook.
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Once squash is fork tender, transfer to large bowl and add in black beans, corn, and in 1 cup of prepared enchilada sauce; stir to combine.
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To assemble enchiladas: Add 3/4 cup enchilada sauce to bottom of a 9x13 inch pan and spread around. Warm tortillas in microwave for 30 seconds so that they are easier to roll up. If you find them hard to roll, I recommend dipping each tortilla in a bit of the enchilada sauce; this will make it much easier to roll and add flavor, too!
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Add about 1/2 cup of the butternut squash & black bean filling to each tortilla and 1 tablespoon of cheese. Roll each tortilla up and place seam side down in baking pan. Pour remaining enchilada sauce over the top along with remaining cheese.
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Bake for 25-35 minutes or until cheese is melted and the edges of tortillas begin to turn a nice golden brown. Top with extra greek yogurt, avocado slices, cilantro, and green onions, if desired. Makes 6 servings – 2 enchiladas each.