1. The US government did not present any authenticated passenger lists
The primary source used by airlines to locate the next-of-kin of aircraft crash victims is the passenger list (or flight manifest). Passenger lists are also a legal document proving for insurance purposes - that particular individuals boarded an aircraft that subsequently crashed. This is why airlines meticulously check the identities of passengers who board the aircraft. With regard to the four 9/11 flights, American and United Airlines have refused to produce the authentic passenger lists or certified copies thereof. As a consequence, major media outlets published shortly after 9/11 partial and inaccurate lists of passengers, based on hearsay information. The US authorities have also issued inconsistent reports about the number and identities of the alleged hijackers. No document has been issued by the airlines or the US government that certifies the claim that the 19 individuals designated on September 14, 2001 by the FBI as the "hijackers", actually checked-in and boarded the four aircraft that crashed on 9/11.
On 13 September 2001 Attorney General John Ashcroft said that "[b]etween three and six individuals on each of the hijacked airplanes were involved' in the hijackings. On the same day FBI Director Robert Mueller said that a "preliminary investigation indicated 18 hijackers were on the four planes -- five on each of the two planes that crashed into the World Trade Center, and four each on the planes that crashed into the Pentagon and in Pennsylvania'.  A day later the number grew to 19.  On September 14, 2001, the name of Mosear Caned (ph) was released by CNN as one of the suspected hijackers on "a list of names (...) that is supposed to be officially released by justice sometime later today".  His name disappeared a few hours later from the list of suspects and replaced with that of Hani Hanjour when CNN posted a new list of suspects released by the FBI . It was never explained why Caned's name had appeared in the first place and why it was then removed. 
According to the CNN of September 14, 2001, "[f]ederal sources initially identified [Adnan] Bukhari and Ameer Bukhari as possible hijackers who boarded one of the planes that originated in Boston." (emphasis added). Yet, a few hours later, CNN issued the following correction: "Based on information from multiple law enforcement sources, CNN reported that Adnan Bukhari and Ameer Bukhari of Vero Beach Florida, were suspected to be two of the pilots who crashed planes into the World Trade Center. CNN later learned that Adnan Bukhari is still in Florida, where he was questioned by the FBI...Ameer Bukhari died in a small plane crash last year." (emphasis added). These names disappeared from later published passenger lists and replaced by new names.
On the very day of 9/11, the FBI, "which has been combing the passenger manifests of all four planes, was already focused on [Amer] Kamfar" as a suspected hijacker. On September 12, at 8:30 AM, eight FBI agents arrived at the door of Henry Habora in Vero Beach, Florida, supposed to be a neighbour of Kamfar, with a photo of Kamfar and asked if it was the same person.  The name Amer Kamfar, which apparently was also gleaned from a passenger manifest, disappeared from later published lists of suspected hijackers and replaced by another name.
The Washington Post revealed that the original passenger lists did not include the name of Hani Hanjour who later appeared as one of the alleged hijackers. In its Final Edition of 16 September 2001 the paper explained that his name "was not on the American Airlines manifest for [Flight 77] because he may not have had a ticket.' Yet Hanjour's name appears on a purported passenger list of Flight AA77 released later at the Moussaoui trial, suggesting that the belatedly released list does not represent a copy of the original passenger list but one which was manipulated.
On 12 September 2001, various newspapers published partial passenger lists of the crashed flights. These reports included Jude Larsson, 31, and his wife, Natalie, 24, as passengers aboard flight AA11.  Yet on September 18, 2001, the Honolulu Star Bulletin reported that the newspaper had received an email from Jude, apparently alive, notifying of the mistake.  According to the paper, "a person claiming to be with the airlines" called Jude's father, a person described as a "known sculptor" in his community, and informed him that his son and daughter-in-law had been passengers on flight AA11. The names of Jude and Natalie Larson then disappeared from publicized passenger lists. Such a mistake would be unthinkable were media reports be based on the original passenger lists. More bizarre is that the names of Jude and Natalie Larson, whose names are not anymore officially listed as flight AA11 victims, are still listed on the National Obituary Archive list of those who died on 9/11.  According to the webpage of this Archive, the list "is based on authoritative sources, The Associated Press and funeral home records". In addition, a website dedicated to the victims of 9/11, even includes a photograph of Natalie Larson (Los Angeles) attributed to the Associated Press and to the Boston Herald. 
According to New York Times reporter Jere Longman, US authorities and United Airlines initially said there had been forty-five people aboard Flight UA93, then amending the figure to forty-four, claiming that one passenger in coach Marion Britton had bought two tickets.  No evidence was presented to corroborate this explanation.
According to Terry Tyksinski, a longtime flight attendant with United Airlines, a customer service supervisor told her that he had observed two passengers leave Flight 93 after hearing an announcement that there will be a five-minute delay in the plane pushing back from the gate. The two first-class passengers were reportedly of dark complexion, "kind of black, not black." According to Tyksinski, the supervisor noted their names and was subsequently twice interviewed by the FBI.  No other accounts, including the 9/11 Commission Report, mention this incident. As these individuals presumably checked in with a ticket, their names should have been recorded on the original passenger list of Flight 93. Were these names then removed and a new passenger list compiled?
According to a report by American Airlines to the 9/11 Commission dated March 15, 2004, "some passengers" had boarded AA11 "after the aircraft had pushed back from the gate." Nowhere could we found any information who these "passengers" were, whether they were listed on some passenger list, and how they actually were brought to the aircraft after push-back. 
The aforementioned fluctuations in the number and names of the alleged hijackers (and passengers) could not have happened if these declarations had been based on authentic documentation.
In 2006 a seven-page set of faxes purported to represent the original flight manifests was published in a book by Terry McDermott.  These released images are of very bad quality and do not appear to be true copies of the original passenger lists (or flight manifests) for at least three reasons: (1) The displayed images reflect pasting together of various sheets; (2) The lists do not include a signature of any official responsible for their authenticity and are not accompanier by a chain-of-custody report; (3) Ziad Jarrah's name is spelled correctly, whereas in the early days after 9/11, the FBI was referring to him as "Jarrahi' as news reports from the time show; (4) The name of Hani Hanjour appears on the AA77 list, whereas the Washington Post reported that his name was not on the American Airlines manifest for the flight (see above); (5) The FBI, responding on April 4, 2007 to the present author's FOIA request for the release of the original passenger lists, wrote that the requested passenger lists of Flights AA11, AA77, UA93 and UA175 were "available publicly through the internet at the U.S. Department of Justice website".  This website contains exhibits released at the Moussaoui trial. An examination of Exhibit P200054 to which the FBI provided a link revealed that it does not contain at all true passenger lists, merely slickly presented graphics purporting to reflect the original passenger lists. The present author's prior belief expressed in previous versions of this article that the aforementioned faxes had been released at the Moussaoui trial, is therefore wrong. Contrary to widespread belief, nothing resembling true passenger lists was released at the Moussaoui trial. This could explain the discretion surrounding the alleged release of these lists at the trial and the reluctance of mass media to highlight this newly released "evidence".
According to his testimony to the 9/11 Commission, Robert Bonner, "[o]n the morning of 9/11, through an evaluation of data related to the passengers manifest for the four terrorist hijacked aircraft, Customs Office of Intelligence was able to identify the likely terrorist hijackers. Within 45 minutes of the attacks, Customs forwarded the passenger lists with the names of the victims and 19 probable hijackers to the FBI and the intelligence community." According to Richard Clarke, who served under both President Clinton and George W. Bush as National Coordinator for Security and Counterterrorism, he was informed by Dale Watson, counterterrorism chief at FBI, on the morning of 9/11 through a secure telephone line that "[w]e got the passenger manifests from the airlines. We recognize some names, Dick. They're al Qaeda." Clarke adds: "I was stunned, not that the attack was al Qaeda but that there were al Qaeda operatives on board aircraft using names that FBI knew were al Qaeda." It also appears strange that Robert Bonner claims to have received a final list of alleged hijackers with 19 names on the morning of 9/11 while Robert S. Mueller, director of the FBI, still claims two days later that they were only 18.  The documents reportedly received by Robert Bonner and Dale Watson were never shown in public. It is possible in the light of the aforementioned fluctuations in the number and identities of the alleged hijackers - that what they received had been lists of names deemed "passenger lists" or "manifests" prepared in advance of the attacks and revised by the FBI or another government agency for mysterious reasons before their final release on September 14, 2001.
While the names of all passengers, crew and alleged hijackers were publicized shortly after 9/11 in the media, the FBI and the airlines have consistently refused and continue to refuse to demonstrate that they possess authentic, original, passenger lists (flight manifests), of the four 9/11 flights . A typical response for the refusal to provide a copy of authentic passenger lists, is that a "litigation is pending". As the names of all victims and alleged hijackers have been publicized within days after 9/11, no plausible reason exists for refusing to confirm by releasing the original, authentic, documents information that already exists in the public domain, unless that information is corrupted or fabricated. The most plausible explanation for this refusal is that the release of the authentic passenger lists (if they at all exist) might prove that no Muslims (or at least not the 19 Muslims named by the FBI) boarded the four aicraft that crashed on 9/11. This would in turn undermine the official account about the events of September 11.
2. No witnesses to the boarding of the airliners
A second category of evidence to prove that particular individuals have boarded a particular airplane at a particular gate and a specific time, is eyewitness testimony and security video recordings.