Pre-heat the oven to 350 degrees Fahrenheit and prepare a muffin tin that yields 6 large muffins (or 12 small).
In a large mixing bowl, whisk together the oatmeal, ground flax seed, cinnamon, and nutmeg.
In a smaller mixing bowl, whisk together the eggs, apple sauce, milk, oil, and brown sugar. Pour this mixture into the oatmeal mixture and mix until well combined.
Pour the oatmeal mixture into the 6 muffin molds, making sure to evenly distribute the batter.
In another small mixing bowl, combine the flour, chopped pecans, softened butter, and brown sugar together until crumbly. Layer this mixture on top of the portioned oatmeal cups. Using a spatula, press the pecans down into the oatmeal batter.
Bake the oatmeal cups for 15 minutes. Let cool slightly before taking them out of the muffin molds.