It was reported that for several years prior to 9/11 CIA intercepted many different plans to attack USA from radical muslims. Back in 90's muslims indeed tried to bring down one of the twin tower with a truck bomb.
CIA agents thought that by allowing some muslims in they can uncover sleeper cells that came a decade earlier. At one point, those muslims who were monitored (and CIA/FBI monitored thousands) went underground. CIA behaved as a typical government agency. Instead of alerting superiors, they probably decided to fish them out on their own. Government workers always use cover-up and fingerpointing instead of personal responsibility. There was bad communication within agencies and between agencies.
After the attack, CIA, FBI, Pentagon, State Department, top politicians, and big busness connected to Saudi oil decided to keep some details sealed. They simply did not want any personal responsibility or scrutiny. Oil money, career promotions, government pensions, etc were at stake. Some secret agencies probably acted illegaly and overstepped their responsibilities. In addition, Bush re-election was at stake.