Preheat the oven to 400 degrees F. Line 18 muffin cups with paper liners. Whisk the flour, granulated sugar, baking soda, baking powder and salt in a large bowl; make a well in the center.
Wash 2 clementines and cut into 8 pieces each (peel and all); transfer to a blender. Add the milk; blend until smooth. Add the eggs and blend until combined. Pour into the well in the flour mixture, add the melted butter and stir until just combined. The batter will be lumpy.
Divide the batter among the muffin cups, filling them three-quarters of the way. Top evenly with the pomegranate seeds. Bake until the muffins are golden and a toothpick inserted into the center comes out clean, about 20 minutes. Let the muffins cool 5 minutes in the pans, then remove to a rack to cool completely.
Put the confectioners' sugar in a small bowl and squeeze in the juice from half of the remaining clementine. Stir to make a thick glaze, adding the juice from the remaining clementine half as needed. Drizzle the glaze over the muffins and let set 10 minutes.
Be sure to use aluminum-free baking powder for these muffins; aluminum can react with the pomegranates and turn your batter blue!