[Latto]

The game doesn't seem to detect magic stones as actually being in your item belt. If you equip them and go into battle they don't show up at all (if it's just by itself the item menu option doesn't even exist.) Also if you put it in quick slot for use in battle it registers as having 0 items.

[Neus]

I can't reproduce this for all magic stones, however Aerialite was checking an incorrect item type, so that may have been your issue.