The black notes are items from the anime. They are the dark counterpart of the Pink notes.
Unlike the pink notes, those notes have a very dark and evil power. If Kuromi gets 100 of them, My Melody will be destroyed squashed by the anger and nightmares under Kuromi's hands. Each note appears when somebody can't accomplish his or her dreams. Baku eats the note to store them in Season 1, or it was stored inside Kuromi's version of the Melody Box.