Preheat the oven to 375°F (190°C).
Line a 12-cup muffin pan with paper liners or lightly grease the muffin cups.
In a large bowl, whisk together flour, oats, baking soda, baking powder, salt, cinnamon, nutmeg, and ginger.
In a separate bowl, whisk together eggs, brown sugar, maple syrup, vegetable oil, pumpkin puree, vanilla extract, and milk until smooth.
Pour the wet mixture into the dry ingredients.
Gently stir until just combined. Do not overmix.
Fold in the shredded carrots, diced apple, chopped nuts, and raisins if using.
Divide the batter evenly among the muffin cups, filling each about ¾ full.
Sprinkle extra oats or chopped nuts over the tops if desired.
Bake for 18–22 minutes, or until a toothpick inserted into the center comes out clean or with a few moist crumbs.
Let the muffins cool in the pan for 5 minutes.
Transfer to a wire rack and allow them to cool further before serving.