Combine cream cheese, sugar and vanilla extract until smooth. Cover and chill until firm.
Line cookie sheet with parchment paper.
Put seeds, sugar and cinnamon in a medium saucepan over medium heat, stirring constantly until sugar begins to caramelize.
Spread seeds on prepared sheet and allow to cool.Break apart the seeds that are stuck together.
Preheat oven to 350.
Place paper liners in muffin tin(s).
Stir pumpkin, oil, brown sugar and sugar together in a large bowl just until mixed.
Add in eggs, spices, salt, baking soda and half of the flour. Mix until combined.
Add milk and remaining flour. Mix until combined.
Fill each liner about 2/3 full.
Spoon one tablespoon of cream cheese mixture into the middle of each muffin.
Sprinkle with 4-5 pumpkin seeds.
Bake for about 15 minutes, until a toothpick inserted in the muffin portion comes out mostly clean.
Cool before serving.