Emigrant wasn't alone. The article also reports on system glitches at Washington Mutual's website. Some WAMU customers were unable to transfer money or pay bills from their online accounts. According to a WAMU spokesman, the problem wasn't widespread. The cause didn't seem to be known. Unlike Emigrant's problems, WAMU's problems wasn't associated with a site upgrade.
One thing to learn from these problems is to make sure you give yourself some leeway when you pay your bills or transfer money. You can't assume that you'll always be able to access your account without delay. Also, as the article mentions, it doesn't help build confidence in online banking. However, there hasn't been any fraud or lost money, so it shouldn't cause too much concern.