This happens all the time on eBay when auction sellers lose track of their sales. It just shows that the company screwed up; if it happens as a pattern, they're unreliable. If it's just once, it's annoying. eBay and Paypal have methods to handle disputes like this, and you've seen that they work.
I wouldn't write off a company if this occurrence is rare, but make sure they know you're unhappy with the situation so they can fix it.