Especially after the centralization of the American surveillance and enforcement infrastructure in The Patriot Act.
The TLA organizations in the government are rival siblings. If the FBI caught wind of a conspiracy to orchestrate 9/11 perpetrated by the Department of Defense in the newly-authorized data sharing, they'd have run it to ground.
This is not an example of the FBI caught in a conspiracy to orchestrate 9/11. If anything, this is an example of the FBI demonstrating, perhaps, insufficient willingness to pursue investigation into a politically allied nation... Not terribly surprising, because (for starters) the FBI's job is domestic investigation, not international. The CIA or NSA would be in charge of looking into Saudi connections to 9/11.
After the Patriot Act, these responsibilities became intertwined, but in the timeframe the article's describing, the nature of that entwining was nascent, and it's not surprising the FBI would have continued to act like the traditional FBI.
