Mtgox is the giant raging zit on the face of Bitcoin. The software and service are so terribly, inexcusably bad, and they have always been that way. The market price on Mtgox has been artificially high ever since I can remember, because no one can withdraw their money. Users wait for their withdrawals for weeks, and sometimes months. As a result, a dollar in your Mtgox account is worth less than a dollar. Now it is artificially low, because people can't transact Bitcoins either! The other exchanges, meanwhile, tend to agree pretty closely, because it is actually possible to move bitcoins and dollars between them.
Imagine if ETrade, say, was so bad at moving money that you had to pay an extra $100 for a share of Google stock. That's what it's like. Or if everyone used Google's DNS servers but they typically took 3 seconds to respond. And yet people use Mtgox, and talk about it, and it's listed on all the sites and apps that track the market price on different exchanges.
At first, everyone chalked up Mtgox's problems to the sheer difficulty of running a Bitcoin exchange, and then, to the difficulty of running the biggest. Well, now it's no longer the only or the biggest exchange, and no one else is having the same problems, at least at this service-destroying level. I can't comment on the difficulty of establishing relationships with banks to move millions of dollars -- I'm sure it's hard -- but Mtgox has also had a lot of plain old scaling issues, and the transaction load is not even that high by web scaling standards. Last time I checked it was 30 per second or so. Their security is nothing special; they've been hacked before. I have heard only negative things about their engineering competence.
I'm a casual fan of Bitcoin but a big hater of bad software, bad customer service, and companies that act in a sleazy manner. I hope Mtgox dies.