Add onion, green pepper, jalapeno, garlic, black beans, tomatoes, chili powder, cumin, salt, pepper, butternut squash, and chicken broth to slow cooker; stir to combine. Cook on low 8 hours or high for 4 hours. 30 minutes before serving, stir in 1 tablespoon of masa harina. If after 30 minutes, it still needs to be thicker, stir in the other tablespoon.