Using a hand mixer or stand mixer, thoroughly combine the butter and brown sugar in a large bowl.
Beat the eggs, one at a time, into the sugar-butter mixture until combined.Stir the greek yogurt, vanilla extract, and milk into the wet ingredients. In a separate bowl, whisk together the flour, kosher salt, baking powder, baking soda, cinnamon, ground ginger, and nutmeg.
Stir the dry ingredients into the wet ingredients, ¼ cup at a time, until combined.
Stir the shredded carrots into the batter.
Preheat the oven to 350°F.
Spray two baking sheets with non-stick cooking spray. Scoop the batter onto the baking sheets, 2 tablespoons at a time, spacing each scoop 2-3 inches apart.
Bake the cakes for 9-10 minutes total, rotating the baking sheets halfway through.
Allow the cakes to cool for 5 minutes on the baking sheets, then remove to a tray to fully cool.
While the cakes cool, prepare the icing:Using a hand mixer or stand mixer, beat together the cream cheese, softened butter, vanilla extract, and almond extract in a medium bowl.Next, stir the powdered sugar into the icing. Finally, whip the marshmallow fluff into the icing until combined. Chill the cream cheese icing in the refrigerator for 30 minutes before filling the whoopie pies. Lastly, assemble the whoopie pies:Place the cream cheese filling into a large zip top bag or pastry bag. Snip off a small corner of the plastic bag. You can also just spoon the filling onto the cakes.Pipe or spoon 2-3 tablespoons of filling onto the flat side of one of the cakes. Top with another cake, facing the flat side onto the filling. Repeat with the remaining cakes. Serve and enjoy.