It could have simply been stolen from the store. It happens. Most likely, it was a store employee who took it in the first place if it is actually missing, but you can't discount the possibility that it was shoplifted either.
When an item is stolen, it won't minus off the inventory unless a manager corrects the item counts. Counts don't get corrected very often in many stores. Usually, they only thoroughly do inventory once a year (around tax time). Many times, they let such items just stay on the inventory list without correcting it because they are afraid of what their district manager will say about the "missing" items. Too many items missing from the store will affect their operating budget and/or future inventory allotments, so they lie about item counts, which is also known as "cooking the books". It's not legal, but most stores "cook the books" to some extent or another.
There are other reasons the count could be off too. Like 2 of any given item was on the shipping manifest, but only 1 actually came in the box and whoever checked in the box didn't notice the miscount. It could be "lost" in the store somewhere, having fallen into a "quiet place" between the shelves or something. Possibly, it was on reserve for someone who never came to pick it up and it's sitting in limbo in a cabinet somewhere.
Technically, the employees are supposed to write down any inventory discrepancies that may arise during their shift and report it to the manager, but most never do. The managers are supposed to search the store for the missing items, but will usually only do that when it comes to covering their own ass.