Preheat oven to 375°F. Arrange phyllo shells on an un-greased cookie sheet. Then, microwave frozen butternut squash as directed on package. Drain any liquid from the squash and set aside.
In a medium sized skillet, melt butter and sauté the onion for ~5 minutes on medium heat. Stirring occasionally. Onion should become near translucent.
In a medium bowl, mash the butternut squash using a potato masher until somewhat smooth. Then stir in the onions, cheese, sage, and seasonings until nicely incorporated.
Spoon mixture into phyllo shells and bake for 8 minutes. Top with pumpkin seeds and serve warm!
These are best if eaten the same day. Leftovers the next day will be soggy. To make in advance, make the filling and keep separate from the phyllo shells. If you would like the butternut squash filling to be smoother, puree it in a food processor or use an immersion blender to smooth out the filling prior to baking.