I was paranoid about this around a year ago, considering how completely reliant I was on the integrity of ebook-selling websites. How could I know that Amazon or BookBaby or Smashwords were truly reporting accurate sales figures ...?
Of course, as soon as there is one accusation against these sites that they are misreporting sales for their own financial gain then they could experience a serious breach of trust worldwide. Depriving me of a few dollars would hardly be worth their reputation. And they make enough money already with that long tail of theirs.