I'm currently having this problem as well, my magician now has 3 boxes of mystery, and stage props are being really weird, after setting up a stage at one venue it gave me the venues props as if they were mine, also got half my stage set up and half the old one on stage at the same time after leaving buy mode.
It's a complete muddle to be honest, I played a singer in the past and had no problems, this game it's nothing but glitches, I have three performers in the same house, singer, acrobat and magician each has their own stage set up but I have to redo it each performance as it keeps adding the others props to the stage as well when I exit buy mode if they performed there last.
Master controller has a sort inventory and sell item function but the boxes don't show up in the list of inventory. And errortrap and overwatch haven't found anything either, it's odd but the extra boxes don't bother me so much as my muddled stages.