Heat 1 tablespoon oil in a large skillet over medium-high heat. Add the garlic and anchovy filets and sauté until the anchovies have dissolved.
Add the diced tomatoes and bring to a simmer. Add the capers, olives, and red pepper flakes to the skillet and reduce the heat to medium-low. Season with salt and pepper and let simmer for about 10 minutes, adding the spiralized butternut squash noodles about halfway through.
While the sauce is simmering, heat the remaining oil in a large heavy-bottomed skillet over high heat. Once hot, add the shrimp and cook until the shrimp turn pink and are almost cooked through, about 3 minutes. Transfer the shrimp to the tomato sauce to finish cooking and return the skillet to the heat. Add the scallops and sear for about 1½ minutes per side, then remove from heat.
Add the chopped parsley to the tomato sauce and stir. Once the butternut squash noodles have become al dente, serve the puttanesca in individual serving bowls and top with a few seared diver scallops. Serve immediately.