User blog comment:UnboundIsaac/Oh No!/@comment-24058253-20150419195115/@comment-24821572-20150420090238

It depends on the slot of the bait. Baits, like ammo that is not in the ammo slot, get used starting from top left, to the right, moving down. I'm guessing you left it to be the first bait in use. Next time, just move the truffle worm to the bottom right and place other baits in the top left under the hotbar to prevent another accident.