Preheat the oven to 350F. Place the phyllo pastry cups on a baking sheet. Otherwise grease a mini cupcake pan.
Heat oil in a skillet, add the onion, peppers, garlic and cook till tender, about 6~8 minutes. Season with salt and pepper. Cool slightly.
Whisk the eggs, milk and season with salt & pepper. Keep in mind that the veggies are also seasoned with salt - so go easy on salt. Stir in cheese, if using. Add the cooked veggies and mix well.
Put about 1tbsp of the egg mixture in the pastry cups. If using cupcake pan, fill them 2/3rds full with the mixture and bake for 8~10 minutes or until the eggs are set and a cake tester inserted into the center comes out clean.
Serve warm or at room temperature.