Preheat the oven to 350 degrees F (175 degrees C). Grease 18 muffin cups or line cups with paper liners.

Sift 2 1/2 cups flour, 2 cups sugar, pumpkin pie spice, baking soda, and salt together into a bowl. Combine pumpkin purée, oil, and eggs in a separate bowl; stir into flour mixture until batter is just moistened. Fold in apples.

Divide batter among the prepared muffin cups, filling each to the top.

Whisk remaining 1/4 cup sugar, 2 tablespoons flour, and cinnamon together in a bowl; cut in butter with 2 knives or a pastry blender until mixture resembles coarse crumbs. Sprinkle cinnamon topping evenly over muffin batter.

Bake in the preheated oven until a toothpick inserted into muffins comes out clean, 35 to 40 minutes.