Arrange a rack in center of oven; preheat to 350°. Grease an 11" x 7" casserole dish with cooking spray.
In a large skillet over medium heat, heat oil. Add onion; season with ½ tsp. salt. Cook, stirring occasionally, until just softened, 5 to 6 minutes. Add garlic and cook, stirring, until fragrant, about 1 minute more.
Add beans, chiles, chili powder, cumin, and ¼ c. water and stir until combined. Add cream cheese and stir until melted; season with salt, if needed. Let cool slightly.
On a clean work surface, lay 1 corn tortilla. Spread ¼ c. filling in a line down the center. Top filling with 1 Tbsp. cheese. Roll up, leaving the ends open. Repeat with remaining tortillas and filling.
Spread ¾ c. enchilada sauce on bottom of prepared dish. Arrange rolled tortillas in a row on top of sauce. Top with remaining 1 c. enchilada sauce and sprinkle with remaining ¾ c. cheese.
Bake enchiladas until warmed through and cheese is melted, 25 to 30 minutes.
Top with jalapeños and cilantro. Serve warm.
