Only did it to me when I finished a book and the stats upgraded. Is that what's happening? You'll see the same thing with equipment when you meld materia to it, as far as the game's concerned, it's a different weapon/item if the stats change.
Applying glamours does the same thing.
Could just be a bug though? Dunno for sure. Certainly doesn't happen to me unless I've done one of the above.
Edited, Jun 12th 2014 9:06am by blowfin