Quotes from the book, p.148 (EDIT: These quotes are in the article here also!!):

"What Serge did not yet know was that Goldman has discovered his downloads- of what appeared to be the code they used for their proprietary high speed trading stock market trading- just a few days earlier, even though Serge had sent himself the first batch of code months ago. They'd called the FBI in haste and had put McSwain [FBI agent who arrested Serge] through what amounted to a crash course in high-frequency trading and computer programming. McSwain later concluded that he didn't seek out independent expert advice to study the code that Serge Aleynikov had taken, or seek to find out why he might have taken it. "I relied on statements from Goldman employees", he said. He had no idea himself of the value of the stolen code ("representatives of Goldman told me it was worth a lot of money"),or if any of it was actually all that special ("representatives of Goldman told us there were trade secrets in the code")."

"The FBI's investigation before the arrest consisted of Goldman explaining some extremely complicated stuff to McSwain that he admitted that he didn't fully understand- but trusted that Goldman did. Forty-eight hours after Goldman called the FBI, McSwain arrested Serge."

So effectively Goldman got Serge arrested, using a clueless agent as a pawn. Some of the code was originally open source, none of the code involved trading strategies (the really valuable stuff) and Goldman's word was enough to convince the FBI that Serge was a dangerous criminal and a flight risk, and ruined his life.