Strange article. Lots of text but missing the main thing I was looking for. What kind "erroneus trades"? where did the money go? If you buy stock at the market you did not intend to buy, why not just sell them the next day?
Seems like maybe they couldn't hold on to the stock for long enough to unload the enormous volume they were dealing with. It sounded like at one point they were doing AS MUCH VOLUME AS EVERYONE ELSE on the exchange combined.
Knight has different programs running. It was handling >10% of all NYSE, so it must have been running a lot of servers. When the berserk algorithm wanted to buy or sell a stock where Knight was the only "market-maker", another Knight server would usually intercept the order after it had been posted on the exchange. Here's one way it might have happened: http://www.nanex.net/aqck2/3525.html
Essentially, they were buying high and selling low. Many times a second.