I'd like to find out the details, if you have a link or something. I have never been able to find any evidence that Mohammad Atta had ever been arrested for anything.
Apparently there was some guy with a similar name (Mahmoud Atta, a naturalized citizen from Pakistan) who was arrested in New York in 1987, but they've determined that it wasn't the same guy.
Atta and one of his henchmen left a small plane on the runway at a small Florida airport, a violation of FAA regulations. The FAA investigated, and obtained Atta's name and Florida address. They did nothing, even though abandoning a craft on a working runway is a serious violation.
There were at least two other incidents where Atta ran up against federal authorities, but no one touched him.
Louis Freeh told the US Senate that the FBI was already monitoring the Muslim terrorist cells in the US in 1999, but claimed they were not a threat to the United States. The FBI already has enough powers to have dealt with terrorist cells in the US years ago. They do not need further powers, and many of the street agents do not want those powers.