In a large skillet, heat the olive oil over medium-high heat. Once the oil begins to shimmer, add the garlic and onion. Cook until the onions are softened and beginning to brown, approximately 5 minutes.
Add the cherry tomatoes to the skillet and cook until softened, approximately 5 minutes. Add the basil, oregano, salt, pepper and tomato puree to the skillet. Stir to combine and cook for about 6 to 10 minutes to develop the flavors of the sauce.
Add the chopped zucchini and yellow squash. Turn heat down to medium and cover and cook until the zucchini and squash are fork tender, approximately 10 minutes. Finally, add the partially cooked penned pasta. Give the skillet a good couple of tosses (or stir a few times). Continue to cook over medium heat until the pasta is cooked through, approximately 1 to 2 minutes.
Serve immediately with crumbled goat cheese on top.