Second, there were restrictions on the sharing of information.
The Watergate-era investigations of government abuses of power led to the adoption (1976, 1983) of highly-restrictive rules for domestic intelligence gathering.
In addition, in 1978 Congress passed the Foreign Intelligence Surveillance Act (FISA) that controlled domestic intelligence gathering directed against a foreign power, usually by the FBI. The Justice Department’s Office of Intelligence Policy and Review (OIPR) took charge of presenting applications for a FISA warrant to the FISA court. The Justice Department’s initial interpretation of the law limited co-operation between criminal prosecutors and the FBI agents gathering FISA information, but in 1994-1995 the Clinton Administration’s Justice Department (acting head of OIPR Richard Scruggs, Deputy Attorney General Jamie Gorelick) further tightened restrictions on contact between the FBI and prosecutors in national security cases. (p. 115.)
“These  procedures were almost immediately misunderstood and misapplied.” (p. 115.) OIPR then bullied the FBI and Criminal Division prosecutors into compliance with this “misunderstanding” of what the procedures actually required. Reviews of these issues in 1999, 2000, and 2001 all concluded that the 1995 procedures were being misapplied to the detriment of national security, but no one did anything to correct the problem. (p. 116.) [NB: Neither Attorney General Janet Reno nor Gorelick tried to correct what the 9/11 Report later characterized as a “misunderstanding.”]
As a result, FBI agents working on intelligence matters communicated but little with both prosecutors and with FBI agents working on criminal matters, although they did pick up lots of useful information from their contacts with the NSA and the CIA. FBI counterintelligence became a sort of black hole in the Justice Department. (p. 116.)
Third, there was a sort of autism prevalent in the FBI. “The FBI simply did not produce the kind of intelligence reports that other agencies routinely wrote and disseminated. As law enforcement officers, Bureau agents tended to write up only witness interviews. Written cases analysis usually occurred only in memoranda to supervisors requesting authority to initiate or expand an investigation.” (p. 259.)
Fourth, Louis Freeh did not communicate with President Clinton. (p. 513.) [NB: I don’t know if this is a reflection of the on-going investigations of Clinton? Somebody needed to give up in the scandals for the good of the country.]
Other Law Enforcement Agencies. “Before 9/11, with the exception of one portion of the FBI [essentially the New York City field office], very little of the sprawling U.S. law enforcement community was engaged in countering terrorism.” (p. 120.) The Department of Justice has the U.S. Marshals Service and the Drug Enforcement Agency; the Treasury Department has the Secret Service, the Customs Service, and the Bureau of Alcohol, Tobacco, and Firearms. The Immigration and Naturalization Service (INS) was swamped trying to deal with the flood of both legal aliens (requiring naturalization) and illegal aliens (flooding in over the southern border). The INS was woefully under-funded relative to its responsibilities. Although the INS attempted to respond to terrorism after the 1993 WTC bombing, “might have been” horror stories abound. (pp. 118-120.)