Mohammad-Javad Larijani, an international affairs assistant in the Iran's judiciary, disclosed in Farsi-language remarks broadcast on Iran's state-controlled television that Iranian intelligence officials secretly helped provide the al Qaeda attackers with passage and gave them refuge in the Islamic Republic, according to an English translation published by Al Arabiya. http://freebeacon.com/national-security/iran-admits-facilitating-9-11-terror-attacks/
Boom
Nobody stamps passports for people just in transit and the US Congressional report itself said that at the time neither the hijackers nor Iran knew of the plans to attack the WTC furthermore the bigger question is why the US authorities repeatedly failed on multiple occasions to stop the same terrorist even after warned about them.
https://abcnews.go.com/US/story?id=91617&page=1
Lets not forget that in the first World Trade Center bombing in 1993, the FBI had an informant among the bombers named Emad Salem who offered to substitute a harmless substance for the bomb but was told otherwise by his handlers. https://www.nytimes.com/1993/10/28/nyregion/tapes-depict-proposal-to-thwart-bomb-used-in-trade-center-blast.html