The film shows the U.S. intelligence figuring out all or most of the Al-Qaeda hijackers before President Bush gets to the military base in Nebraska. In reality, they had only figured out three of them by the time he attended the virtual meeting (the sixteen other hijackers were later figured out).
Some of the scenes of the events happening on September 11th are shown in the wrong time sequence. Some examples are: Vice-President Dick Cheney is shown being brought down to the bunker minutes after Flight 77 crashed into the Pentagon, in reality it was minutes before (as the plane was rogue and not responding). Flight 93 is shown crashing (disappearing on radar) after the North Tower of the WTC collapsed, it actually crashed 25 minutes before.
Most of the government officials are seated in different seats then they were in the actual meetings (as shown in the actual photos).
In the meeting at the Offutt base in Nebraska a few of the figures are missing from the virtual meeting. Condoleezza Rice and Stephen Hadley (the latter is not portrayed in the film) participated with Dick Cheney. VCJCS Richard Myers participated with Donald Rumsfeld. Deputy Sec. of State Richard Armitage was on a screen from the State Department. Additionally, the base Admiral Richard Mies sat at the table with President Bush and Chief of Staff Andy Card, he is not depicted.
The Marine sentries at the White House are missing their covers (i.e. hats), which they should be wearing when on duty at their posts.
The stock news footage combined with the reenactments are not exactly matching at several times.
Several characters pronounce the country names "Iraq" and "Iran" wrong most of the time (the former is pronounced "Ee-Rock" and not "Aye-Rack", the latter is pronounced "Ee-Ron" and not "Aye-Ran"). However, since those countries have never been the big allies of America, the politicians like to disrespect them by deliberately mispronouncing their names.
The Navy sailors at the Pentagon breakfast and at Camp David are wearing the "Salt-and-Pepper" uniform (black pants with white shirt) that was discontinued in the 1980s.
A young Navy sailor at the Pentagon is wearing a United Nations Korea Medal ribbon on his shirt, which is from the 1950s.
USAF officer McGrath on Air Force One wears a United Nations Korea Medal on his uniform jacket, which is from the 1950s.
One of the Army soldiers at Barksdale AFB is armed with an M16A1 rifle; by 2001 that rifle had been replaced by the M16A2.
The news footage of a section of the Pentagon (where it was hit by the plane) is shown collapsing before the south tower of the WTC fully collapses. In actual time, it collapsed after the south tower went down, but before the north tower did.
Washington, D.C. police (MPDC) are seen on the Pentagon grounds immediately after it is attacked by the hijacked plane; the Pentagon is in Arlington County, Virginia so the Arlington County Police (ACPD) would have been there instead immediately after the plane crash.
Bush and several others pronounce "PEOC" (which stands for "Presidential Emergency Operations Centre") as "P-E-O-C-" every time, it's usually pronounced as one word (acronym) rather than as individual letters (initialism).
All the main Joint Chiefs of Staff appear to be present at Bush's meeting with his National Security Council on the night of September 11th. The only Joint Chiefs of Staff who attended were Chairman Hugh Shelton and Vice-Chairman Richard Myers.
When on the phone with Rice, Bush says "DEFCON Delta" when he should have said "THREATCON Delta". Later on in the film, Rice makes the same mistake as well, saying "DEFCON Delta" instead of "THREATCON Delta".
The then-assisstant communications director Dan Bartlett is later depicted in the film. He was however not seen earlier with the team when at Florida nor in Air Force One which he historically participated with.