The evidence: You might have heard the popular internet phrase, 'Jet fuel can't melt steel beams.' Essentially - and correctly - truthers believe jet fuel can't burn hot enough to melt steel beams.
The Twin Towers also fell relatively straight down, like you see in a controlled demolition; and a third building - WTC7 - also collapsed, despite not being hit by a plane.
Lastly, lobbies in both towers were visibly damaged when first responders arrived on the scene, despite the planes crashing into the buildings dozens of stories above.
The truth: Jet fuel can't melt steel beams, but it can burn hot enough to severely weaken them. A Popular Mechanics article first published around the time Loose Change came out said at 600C, steel would lose about 50 percent of its strength - and jet fuel can burn a lot hotter than that.
WTC7 took a hit from falling debris, as well as experienced its own blaze that wasn't attended to, firefighters busy with everything else that was going on.
And the lobbies were damaged because much-burning fuel fell down the elevator shafts, sending some elevators plummeting to the ground.
"The doors cracked open on the lobby floor and flames came out and people died," one expert told Popular Mechanics.
The Pentagon was hit by a missile, not a plane
While there's video of both plane impacts in New York, some have claimed the Pentagon was actually struck by a missile.
The evidence: There is no good footage of the Pentagon strike, with security video showing little but a white blur before an explosion. The hole punched into the side of the building also appeared too small to have been made by a Boeing 757.
The truth: It was a plane. Its wreckage was found - including the black box. But that's not all.
"I held parts of uniforms from crew members in my hands, including body parts," a blast expert told Popular Mechanics.
The magazine also pointed out a crashing jet "doesn't punch a cartoon-like outline of itself into a reinforced concrete building". One wing broke off when the plane hit the ground, and the other was broken off by one of the recently-renovated Pentagon's load-bearing columns. The fuselage would have been "in a state closer to a liquid than a solid mass" due to the impact.
Flight 93 was shot down
One of the four hijacked planes didn't make it to the terrorists' target, with passengers fighting the terrorists and the plane crashing into a Pennsylvania field.
But truthers maintain that's not what happened, some instead claiming it was shot down by the US government.
The evidence: A military jet was seen in the same area as Flight 93 beforehand; parts of the plane were found far from the crash site; President George W Bush gave the order to shoot down hijacked planes after the Twin Towers were hit.
The truth: It's not known exactly what happened, but cockpit recordings suggest the account shown in film United 93 to be largely accurate - the passengers knew terror attacks had been carried out in New York and at the Pentagon, so decided to fight the hijackers rather than let them continue to their target.
It's generally believed the hijackers deliberately crashed the plane, rather than let the passengers take control.
Experts said at the speed the plane was travelling, the fact debris was found hundreds of metres from the impact site wasn't surprising at all.
The US let the attacks happen
Some believe the US government turned a blind eye, knowing a devastating attack would give them pretext to invade the Middle East - or that it was an inside job.
Evidence: In hindsight, there were plenty of warnings an attack like 9/11 would happen - as early as 1998 there was talk of hijacking planes.
The US had previously considered staging 'false flag' terror attacks during the Cold War and blaming them on Cuba, to justify an invasion of the nearby Communist nation.
There was also an "abnormal" amount of trading in shares of American and United Airlines, and defence contractors, in the days leading up to the attack.
And the authorities took a suspiciously long time to respond to the emergency once the planes had been hijacked.
The truth: The 9/11 Commission found no evidence the trading was suspicious, with most of it being traced back to a single investor.
The planes couldn't be tracked once they'd been hijacked, as the terrorists turned off the transponders.
NORAD didn't track airspace over the US at the time, and literally had to wait for phone calls from local civilian operators before it knew anything was amiss. Its focus was outwards "like a doughnut" around the country, one expert said.
As for deliberately ignoring the months of warnings beforehand, that's generally been considered incompetence, rather than anything sinister.
A warning in August was dismissed by National Security Adviser Condoleeza Rice because it was non-specific, and "did not raise the possibility that terrorists might use airplanes as missiles". In July Defense Secretary Donald Rumsfeld rejected evidence suggesting an attack was likely, believing it was intended just to gauge how the US would respond.
In April, a NORAD wargame simulation in which a plane would crash into the Pentagon was rejected as "unrealistic".
The passengers from Flight 11 and Flight 175 were put on Flight 93 and killed
Now we're getting into truly wild territory. There's a theory out there that not just the Pentagon was hit by a missile, but the Twin Towers too. This theory holds that the two jets which hit the towers were actually missiles, and the passengers who were supposed to be on those planes were secretly bundled onto Flight 93, which was then deliberately crashed, disposing of the eyewitness evidence.
Evidence: None, really - just a lot of chatter in internet forums.
The truth: The biggest argument against this is the same used against claims the US didn't go to the moon - the sheer scale of the cover-up would be impossible. It would require thousands of people working together, not a single one of them screwing up or spilling the beans - something no government is arguably capable of.
The aftermath
Even the makers of Loose Change would go on to admit they made several errors.
"We know there are errors in the documentary, and we've actually left them in there so that people discredit us and do the research for themselves," one of the makers once said.
