A difference at the end of a stocktake rarely means someone took the goods. The far more common reason is that stock left the warehouse without a record: a sample was given away, a return came back, or two people entered the same shipment twice.
The most practical way to reduce unrecorded movements is to tie stock to documents. Goods leave when a delivery note is issued and arrive when a purchase invoice is approved. Wherever stock is "adjusted" by hand, differences accumulate.
The second point is not deducting the same thing twice. When you invoice goods you already shipped on a delivery note, stock must not drop again. Kumpara keeps the total stock movement for a sales line at the greater of the shipped and invoiced quantities, with each step posting only the difference.
Finally, record the stocktake difference as a movement too. "It was corrected" is not enough — when, by whom and by how much should be visible. Otherwise you will be asking the same question again at the next count.