I set up that the player gets bombs through initial data, but when I tried to use them in the game, Link didn't do anything. But after buying more bombs at a shop, Link was able to use bombs normally. The same (or similar) bug happened when I "cheated" some super bombs into my inventory (Refill Bombs). I was unable to use the super bombs and when I went into "Link Data" and checked the unchecked box (!) for super bombs and tried to use them, ZC crashed back to the desktop. Hope this helps you find and kill this annoying bug.
-Turb