I recently watched United 93, which depicts the events on the plane that crashed in Pennsylvania. I wonder how much of it is speculation and how much is probably true. For example, how exactly did the hijacking occur? Do we know with certainty that one of the hijackers had a fake bomb? How do we know they used box cutters? How do we know the pilots died? How do we know they put on bandanas? I could go on.
What can we say with certainty about the hijackings and what is our basis for knowing this?
A lot of what we know comes from recordings from phone calls from the planes and from transmissions send in error by the suicide pilots themselves. There might be more evidence from other sources, but not all of it can be accessed by the public, and not every victim`s family has agreed to let the public listen to the private last calls of their loved ones. Still, especially flights and their communications are always extremely well recorded, especially communications between controllers and pilots. And many calls coming in to other first responders are also recorded for later evaluation and potential evidence for crimes. In this case, both created a host of audioevidence for what has been going on in these flights, on the ground, and in the Towers. Research took nearly all hard evidence of what has been going on during these first moments from these audio recordings.
There was a flight attendant named Betty Ong on Flight 11, who made a several minute long call to her superiors from an onboard phone and transmitted what they had witnessed during the highjacking and what had happened to the Pilots from her point of view. Among other vital information, she descibed how the attackers had stabbed another member of the crew, the purser, or highest ranking cabin crew, and other people, and that she didn`t know who had attacked. So we know they had knives of some form. She also explained that the highjackers had used mace or something similiar to attack passengers and crew in first class and business class, and that the pilots no longer answered to inflight communications or opened the door. In her recording you can hear how she talked to other crew members and passengers in the background to gather information, and how she communicated what was going on from shortly after the highjacking to the point of impact in the building when the call cuts off. From this we know that, at least in this flight, the passengers new that something was going on, but they probably weren`t aware of what exactly was going to happen until the last moment. We know the weapons must have been blades of some form, and that there must have been a fight.
Not all of her call has been published, but during the extensive hearings in the time after 9/11 at least the abovementioned parts were extensively studied and have been used in documentaries and media ever since then. So you might be able to find either parts of the real audio or at least the corresponding documentaries concerning the recordings very easily.
Another audioevidence from the same flight has been a transmission most likely made in error by one of the terrorists, who might have meant to adress the passengers via onboard communication to calm them down. Instead, he spoke to an aircontroller who also answered but the pilot, at this point, might not have heard him, or not recognized the voice to be directed at him. From this call we know that they might have tried to tell the passengers to remain calm and that they will return to the airport, and that it was very likely they purposefully tried to keep the passengers calm to do their attack without further fights.
There is a lot of similar audioevidence from the other flights, but especially the recordings for Flight 93 have been numerous due to the length of the actual flight. For example, there is only a very short window between the last communication of controllers with the real pilots, and audio that may have been from the actual highjacking or shortly afterwards. The pilots must have made two attempts to communicate at this moment, and you can understand even something like "we`re going to die here" on the call, but afterwards the pilots no longer answered to the controllers - from the time between both attempts at communication we do have evidence for a longer struggle in the cockpit, too. A few minutes later, again, the highjackers transmitted in error, most likely to the passengers, and stated they had a bomb on board and the passengers should remain calm while the highjacker`s demands would be communicated.
Almost everything else we know of that flight came from the numerous calls that happened between the passengers and the ground during the roughly 60 minutes between the highjacking and the impact on the ground. It may be the fact that these people had this long of a time to call home that allowed movie makers to reconstruct a very detailed image of what must have been going on, but much what went on between the calls may be speculation to have everything fit togther into a movie. However, it is a fact that the passengers, opposite to those of the other aircraft, had enough time to learn about what was going on from the people they called, since by that point the other three aircraft were already down and a number of newreports showed on live TV what was going on, reacted to what was going on, and communicated that they planned to fight back with the people on the ground.
As for the Black boxes, flight data recorder and voice recorder, and their data; those from Flights 11 and 175 have been destroyed in the collapse of the World Trade Center; from Flight 77, the one hitting the pentagon, only the flight data recorder could be salvaged while the voice recorder was too badly burned; and for Flight 93, both black boxes could be recovered. A transcript for the audio recorder can be found on the National Park Service website dedicated to Flight 93.
So, basically, thanks to a rather large amount of audioevidence, at least part of what has been happening inside the aircraft during the minutes prior to their respective crashes, has been actually recorded and allows researches to construct what exactly must have happened. The movie may base on that, but as I stated, most likely with some liberties to make it into consumable storytelling.
Edit: Addition in regards to data recorders.
I'd like to add a little more to /u/Technical-Doubt2076's superb answer.
Much of what we know are first person accounts via audio but we also have additional information on what was planned to happen during the hijacking based on interviews and interrogations with the planners of 9/11 planners, such as Tawfiq bin Attash (AKA Khallad).
Specifically we have people on the planes reporting that the hijackers claim to have bombs, and eyewitness accounts of knives, boxcutters, and red bandanas.
At least 10 passengers and two crew members shared vital information with family, friends, colleagues, or others on the ground. All understood the flight [93] had been hijacked. They said the hijackers wielded knives and claimed to have a bomb. The hijackers were wearing red bandanas, and they forced the passengers to the back of the aircraft.^1
With few exceptions, the film Flight 93 strove to document what happened on the plane realistically and hewed to facts rather than entertaining conjecture. As an example, there was a single report on flight 93 of a gun, but there exist no other evidence in the form of recordings, security, or in the wreckage of any of the 9/11 flights that guns were used. Conversely, there was no evidence that Christian Adams, a passenger ever attempted to appease the hijackers as presented in the film, so that seems to have been creative license. There are some minor quibbles about when calls were made and such, but nothing that alters the events on board.
On a side note about the making of the film, the producers choose to use actors with very little screen time so viewers would focus on a movie star, but rather see the actors more like regulars people in this situation, which I thought was neat.