I just tried to recreate these in my game with no luck. Bought hay from Marnie just fine and bait makers gave bait just fine as well.
What happens to me constantly is hijinks with the "Add to existing stacks" button when you've got a chest open. I'm always using that to quickly empty my inventory, but sometimes I'll have like 1 bait in one of my chests for some reason, and without realizing it, I'll place all my bait in there without meaning to. Then see it's missing while fishing and wonder what the heck happened, and find it back in a chest at home later.