Preheat the oven to 375ºF. Coat a 9x13 baking dish with cooking spray. Set aside.
In a medium skillet, heat olive oil over medium heat. Add onions, red pepper, and green pepper. Cook, stirring occasionally, until softened, 7-10 minutes. Stir in green chiles, black beans, and pinto beans and cook until heated through. Remove from heat and add the cilantro and salt to taste.
Pour a small amount of enchilada sauce in the bottom of the prepared baking dish and spread evenly. Top with 6 of the corn tortillas and half the bean mixture. Add half the cheese and pour half the remaining enchilada sauce over the top. Top with the remaining tortillas and bean mixture. Pour the remaining enchilada sauce evenly over the top and finish with the remaining cheese.
Bake, uncovered, until bubbly and just beginning to brown, 20-25 minutes. Serve with sour cream, lime juice, and tortilla chips if desired.