Preheat the oven to 425 degrees F. Peel and dice butternut squash. Melt 2 tablespoons of butter in a large pot over medium heat. Add the onion, fennel seeds and garlic and cook until soft, about 5 minutes. Stir in the ginger, nutmeg, turmeric, cumin, coriander garam masala, and salt and pepper to taste and cook until toasted, 1 more minute.
Add the diced butternut squash, broth and 2 cups water to the pot, cover and bring to a boil over medium-high heat. Reduce the heat to medium low and stir in the applesauce. Simmer, covered, until the squash is soft, about 20 minutes. Puree the soup with a blender until smooth. Season with salt and pepper; keep warm.
Peel , core and dice the apple, heat the remaining 1 tablespoon butter in a skillet over medium heat. Add the apples, stirring, until browned; remove from the heat and add the vinegar. Top with the cilantro. Fold the mixture into the soup and serve hot.