It was a critical problem why the CIA did not stop the Sep 11 attack, even though some of their directors possessed the exact intel of this terrorist act.
This issue is related to the fundamental of the intelligence organization that they require the enemy at any moment. If not, they lose their raison d’etre, which triggers a shrinkage of their capability. The CIA and other Western intelligence organizations won the cold war, but their victory was translated into a reduction of their headcounts and budgets.
One of their options to counter this move was to create the enemy by themselves, which kept their organization intact. I was one of the targets for this operation mainly by the Japanese police intelligence, but definitely, the CIA did the same to others.
There was another option for this, which was to leave the terrorists at large. The CIA could have created a necessity for themselves just not to stop the terrorist act in the US even though noticed beforehand.
The intelligence agency has originally been accustomed to leave the critical issue without interception as it is one of the protocol to grasp the whole figure of the opposed organization. It used to be a spy agency in the enemy countries, though including the crime organization and the terrorist group.
This protocol is escalated to hire some members of the targeted organization and ignore their terrorist conducts to support their promotion within the enemy. This operation is justified by the logic that the terrorist group is easily contained once their decision is made by their assets.
I assume the CIA should have perceived that the Sep 11 attack was one of their strategies for their survivals. If the sizable terror occurs, the necessity of the intelligence job is increased, which was actually what happened after the Sep 11 attack that they expanded their authority, headcount and budget.
There was a possibility that they had not assumed the outcome was so enormous to kill thousands of people. They definitely realized that the terrorist would avail the airplane in advance as they monitored the attackers who had the flight training in the US. However, it was hard to forecast the towers were collapsed in that manner, hence the damage was more than they expected.
Having said that, my assumption was still wishful as the leaders at the CIA or other intelligence organization have behaved not to care about the death count as far as they have secured their organizations and their loyal subordinates. That means, they also did not care how many people died from the Sep 11 attack, as far as it was favorable to their organization.