Bring a large pot of lightly salted water to a boil; add penne and cook, stirring occasionally, until tender yet firm to the bite, about 11 minutes. Drain.
Cook and stir ground beef and Italian sausage in a skillet until browned and crumbly, 8 to 10 minutes. Transfer to a bowl using a slotted spoon. Drain excess grease, reserving 1 tablespoon in the skillet.
Cook and stir zucchini and yellow squash in the reserved grease until slightly softened, about 5 minutes.
Preheat oven to 350 degrees F (175 degrees C). Spread 3/4 cup pasta sauce in the bottom of a 9x11-inch casserole dish.
Pour remaining pasta sauce into a Dutch oven over medium heat. Stir in zucchini and yellow squash, whole olives, and sliced olives. Cook and stir until pasta sauce is heated through, about 10 minutes.
Layer half of the ground meat mixture, penne, hot pasta sauce, Cheddar cheese, and mozzarella cheese over the pasta sauce in the casserole dish. Repeat layers once more.
Bake in the preheated oven until cheese is melted and layers are heated through, about 30 minutes.