Preheat oven to 375 degrees F (190 degrees C). Prepare muffin cups with cooking spray.

Heat a large skillet over medium-high heat. Cook and stir beef in the hot skillet until browned and crumbly, 5 to 7 minutes; season with salt and pepper. Drain and discard grease from beef.

Cut wonton wrappers into 2 1/4-inch circles with a biscuit cutter. Press one wonton into the bottom of each muffin cup. Sprinkle even amounts of Parmesan cheese, mozzarella cheese, and ricotta cheese into each muffin cup; top each portion with even amounts of ground beef and pasta sauce.

Divide 1/2 cup Parmesan cheese, 1/2 cup mozzarella cheese, 1/2 of the ricotta cheese, 1/2 of the ground beef mixture, and 1/2 cup pasta sauce, between the muffin cups and layer, respectively, atop wonton wrapper; repeat layering with remaining wonton wrappers, 1/2 cup Parmesan cheese, 1/2 cup mozzarella cheese, remaining ricotta cheese, remaining ground beef, and remaining pasta sauce. Top "cupcakes" with remaining Parmesan cheese and mozzarella cheese.

Bake in preheated oven until edges of "cupcakes" are browned, 18 to 20 minutes; let rest in tins for 5 minutes before running a knife around the edges to loosen and remove. Garnish with fresh basil to serve.