It's like if you cause an accident while you're driving by breaking the law; you get a traffic citation (and the accompanying fine), even if your car is totaled as a result of the accident, because you did something illegal.
-- Relied on financial risk controls that were not capable of preventing the entry of orders that exceeded pre-set capital thresholds for the firm in the aggregate.
https://www.sec.gov/News/PressRelease/Detail/PressRelease/13...
(The charge also states that Knight violated rules on covering shorts, but I guess this is not so important).
The SEC is quite right to fine firms that have lost money with poor risk controls: the point is that bad risk management can hurt the whole sector. It is like fining a factory owner who lets their plant break pollution regulations.