I haven't thought too much about it but one bad example would be the operator of a large pool like BTCguild would have the advantage of hiding their bids by including their transaction in their next block without transmitting it to the entire network. Or they could "bid up" their own auctions by transmitting a very high bid but then negating it by include a different transaction in their next solved block. Other bidders would see the high bid and try to outbid it while that transaction actually gets rejected, if that makes sense. I'm sure far more clever people could think of more sinister ideas 
BTCguild can do all that, but only if they solve the next block. It's very risky to broadcast fake high bid, if you don't solve the block that amount will be included in the blockchain and forever gone from BTCguild's wallet. I don't believe they would do such things for just any auction. It's questionable also if they have software solution to play with such a things, remember you would have to send fake Merkle tree hash to all your pool miners, different from the publicly broadcasted tree. Members of your mining pool may notice that. I seriously doubt they would risk such things, their reputation and pool earnings a worth to them much more.