This sadly happens a lot in others games, especially in MMOs. You'll traverse one area only to fight a pallet swapped version of something you just beat up. This really does change later on though in the expansions. One other thing to keep in mind that a lot of these monsters you see are iconic enemies often seen in the FF game series. So that is the other reason a lot of them are reused, to give call backs and sense of nostalgia to some.