Put 2 tsp of olive oil and 2 cups of sliced carrots into a large pot, mix, and heat over medium-high heat. Sauté the carrots until tender, about 4-5 minutes. Add 1 cup of diced onions and the diced garlic, mix and sauté for 1-2 minutes.
Reduce the heat to medium, add the ground beef and turkey to the pot and mix breaking it up into smaller pieces. Top the meat with ¾ tsp pepper, 1 tsp of salt, and 1 tsp of dried thyme. Mix and cook until the meat is browned, about 5 minutes.
Add 1 Tbs of coconut flour to the meat and mix. Then add the 4 Tbs of tomato paste, 1 Tbs of apple cider vinegar, 1 tsp of onion powder, and 1 tsp of chili powder to the meat and mix. Add 1.5 cup of chopped tomatoes, mix.
Add 1.5 cup of chicken stock or bone broth and simmer until the sauce reduces to a gravy, about 5-7 minutes.
Pour the shepherd's pie filling into a large pan, 9 in x 13 in. Top the meat in the mashed butternut squash topping, using a spatula to evenly spread it out.
Bake for 20-25 minutes.