They need to distinguish the lures from the bait. I bought crow fly and it has the same identification as say crayfish balls, but it doesn't get used so I assume you only need 1. But the game doesn't tell you anything about that. Even the quest says, "Using Crow Flies" meaning multiple, so I went and spend 7k on 31 crow flies, because I didn't know how many I was going to need to catch the fish, and they were so far away, I figure if I have extras it's okay.
So now I have 31 crow flies in my bag that vendor for 3gil or so each, but cost 240gil... *sigh*
Lures, unlike bait, are not used up if you successfully catch your fish. But if you get a bit and miss it, you can still lose your lure. So it's not a complete waste, you will ever conceivably use them up. 31 will last a good long while though, I bet.