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 head to medium, add the ground beef to the pot and mix breaking it up into smaller pieces. Top the ground beef with 1/2-1 tsp of black pepper (I used 1 tsp bc I liked the added kick), 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 well. Then add the 2 Tbs of tomato paste, 1 Tbs of apple cider vinegar, 1/4 tsp of ground cloves, 1/2 tsp of onion powder, and 1/2 tsp of chili powder to the meat and mix. (Note: if cloves aren't your thing, put a pinch in, but I found this gave it more of a Worcestershire sauce flavor while keeping it Paleo and Whole30). Add 1 cup of chopped tomatoes, mix, and simmer for 2 minutes.
Add 1 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 9in x 13 in glass dish.