Actually almost all of these items are meant to be unobtainable:
Magma Stone - Buck takes it, puts it back, you never get it
Old Charm - You give it to Cynthia
Works/Storage Key - Your meant to get these
Contest Pass - Unneeded as contests are enterable without this
Suite Key - Used for Darkrai, will be released eventually through mystery gift
Loot Sack - You use the treasures pocket underground instead
Rule Book - You set rules when battling or trading with people through wi-fi, so this was scrapped
Red Chain - Team Galaxy get this and it breaks, your character never gets it so it was made unobtainable.
Credit to .Impact for the sig & avy