Bring a large stockpot of water to boil. Cook pasta shells to al dente. Drain and rinse well with cold water to stop the cooking process and prevent pasta shells from sticking together.
In a medium bowl, mix all filling ingredients together until well combined. Stuff cooked pasta shells with filling and set aside.
In an oven-safe skillet on medium-high heat, cook chicken with olive oil, onion, bell peppers, oregano and fennel seeds, until crumbled and golden, about 5 minutes.
Preheat the oven to 400 F. Add tomato sauce, milk, oregano to skillet. Season with salt and pepper to taste. Add stuffed pasta to skillet in an even layer and top with mini bocconcini and red pepper flakes.
Bake in the oven for 15 minutes until bubbling and golden. Remove the skillet from the oven and allow pasta to rest for 5 minutes before plating. Enjoy with mixed greens.