I don't see the motivation for BTC-e to selectively scam. They have a successful trading platform and therefore have a secure income from the fees. Why would they risk that?
It can be an employee of BTC-e who thinks his wages are too low and decides to make some more income.
Of all the main exchanges BTC-e, is the one with the most scam stories.
It doesn't help that the people behind BTC-e are anonymous.