If Link picks up an an ammunition type item that increases his normal bomb supply while he doesn't even have a normal bomb type item, he turns into a black square. But he turns back to normal if he picks up the normal bomb type item afterwards.
Here's a test quest file demonstrating the glitch:
http://www.mediafire.com/?say3w9dw61i1c5j
This quest also ammunition type items that increase super bombs. So if Link picks up a bomb ammo item that increases his super bomb supply while he doesn't have a super bomb type item, the same glitch happens, and he has to pick up the super bomb type item afterwards to turn back to normal.