Preheat oven to 350°. Line muffin tins with liners.
Stir pumpkin, oil, and sugar together in a large bowl. Do this by hand - don’t use a mixer. Stir in eggs, pumpkin pie spice, salt, and baking soda. Stir in 1 cup flour, then stir in milk, then stir in remaining 1 cup flour. Divide evenly among muffin pans, filling each liner 1/2 full.
Stir together cream cheese, sugar, and vanilla. Drop 1 tablespoon onto the top of each muffin. Sprinkle with 4-5 pumpkin seeds, optional.
Bake for about 15 minutes, until a toothpick inserted in the muffin part comes out with just a few crumbs stuck too it.
Cool at least 5 minutes before serving. Store in refrigerator. Muffins can be frozen for quick breakfasts!