The pieces of wood trim are cut differently than the rest of the door. The grain is different.
Wood can be cut "with" or "against" the grain. This produces a fine tight grain or a wild grain. The different pieces have a wild wood grain. There is nothing that you can do about it. Stain highlights whatever wood grain is there. The very light areas are made of harder wood with tight closed pores and the dark areas have open pores, typical of soft wood.
You could try applying another coat of stain to these pieces only and see if it will darken them, blend them better with the rest of the door. Your chances are very slim that this will make much of a difference. With such a wild grain there isn't a whole lot that can be done.