They were never directed to by the Clinton Adm., for whom combating terror "was its highest priority" (Clarke).
The real "problem" and it was not really a problem was that the FBI was created for domestic crime by design. It's focus has always been domestic crime. And it could not exchange information with the CIA. Not at any really beneficial level prior to 9/11. Zelikow said that the CIA and FBI did exchange information at top levels. But that was just not good enough.
9/11 crossed the bounds between federal agencies that handled extra-territorial and territorial information. The CIA and the FBI. They were simply not able from an information technology and information sharing standpoint to work together. They could not by design.
Mr. Zelikow is an academic who like all academics is very good at 20/20 hindsight. He's a smart guy. All these people are smart. But they didn't see the monsters of Allah. Few people did. Certainly not people in Congress, who really should be blamed more than anyone for 9/11. If we want to blame anyone.
The bottom line is that US law enforcement agencies simply did not exchange data. They still do not. Not in a way that would have identified and prevented 9/11.