I've probably mentioned this story here, but my first job out of school was working for a nationally known cash register manufacturer, writing front-end software for the cashiers to use. This didn't happen to me but was told to me by an old-timer my first week there (mid-90s).
A group had done an install at a grocery store. They did in-house testing of the new system, then rolled it out to 1 or 2 lanes to try it out for a few days before upgrading all the lanes with the new system. It was a fairly normal roll-out with a few minor issues, but nothing major.
The day they rolled it out, about 2 or 3 transactions each day started including an extra charge for 10 cents worth of deli meat. This was weird because it would be pretty hard to buy only 10 cents worth of meat, and certainly any deli counter worker who had rung it up would have remembered doing so because it would have been a really bizarre order. None of them had seen such an order come through.
The only thing the transactions had in common was they were paid for with a debit card. Worried about compliance issues and the possibility that there might be a bug in the new card readers, they turned off the debit card functionality. Unfortunately (or fortunately if you work in compliance), it happened again to someone paying with cash. While that was a relief because it meant the card readers were fine, it also meant they had no leads on the problem.
The on-call engineer got called in to work on the problem just before the store closed one night. He checked all the obvious things - problems with the cabling; an incorrect value in the database; some data getting mangled between the cash register and the database; a problem with the scanner; etc. There were no problems he could detect.
In order to keep the last few customers from entering his lane, he moved a shopping cart in front of the lane. In fact he did it to the one next to his as well because he'd be walking around the entire lane working on cabling and such. He crawled under the register to check something things just as the scanner beeped to indicate it detected an item. Sure enough it was for 10 cents worth of meat. He looked around and noticed a mother scolding her child, "Leave to empty carts alone! That lane is closed!" That's when he noticed that the cart had an ad on front of it for some random product. He jiggled the cart, and the scanner beeped again. Another 10 cents of meat.
It turned out the artist who put together the ad thought that the packaging without a barcode on it looked weird, so he grabbed something he had laying around and made a fake barcode that looked similar. By some miracle, the barcode was actually valid and was ringing up 10 cents of deli meat at this store. Mystery solved!