was it a CD? probably was a promotional item, radio stations get CD cases with the bar code punched or the case notched with what appears to be a bandsaw.
More than likely its so that seller could get the rebate. Ebay is full of items like this. People just buy tons of stuff from stores, collect the rebate, then resell them for the price they paid for them. Instant profit. I've never had a problem with it as long as you are aware you can't get any manufacturer rebates.
Best Buy will take back items without the UPC symbol, though. That's probably why if you buy and openbox item that has a rebate, they just sell it for the price minus rebate. That way, you get the discount anyway (and if you're lucky to get one with the UPC on it, you can collect again).
**Edit** Sorry, misread your post. If the UPC just has a hole in it, then yeah it's probably a promotional item. If the UPC is completely missing, then my answer above is probably most likely.