I don't think that there's any loot that doesn't appear again with some more monsters running around Ivalice. I'll read up on in a bit more in-depth though, and give you a more definite answer, but my gut feeling says no.

I know that there's certain weapons that you have to steal in order to get them, and you really have only one shot at getting them. The Genji armor comes to mind. If you don't get it during the hunt "Battle On the Big Bridge", then you can say "Bye bye" to ever getting it in the game. But as for the loot, even if you miss stealing it from rare monsters, I'm pretty sure it appears elsewhere in other enemies.