Main terrorist Safarini removes the suicide belt (with explosives tied on it), places it on a seat's armrest near the cockpit on the second floor, but he takes it back from the seat on the first floor where all the passengers were placed and the whole hijacking incident took place.
When the 747 is on the tarmac at Karachi, as one of the hijackers runs up the air-stairs, 9 windows to the upper First Class cabin are visible. Pan Am 747s only had a row of three windows in the upper First Class cabin.
Regular home-drip coffeemakers are visible in the Pan Am airplane galley. In real life, commercial aircraft have special (very expensive) coffeemakers built into their galley shelves, with special safety features such as a pull-down handle to secure the pot during take-off, landing, and turbulence.
The Pan Am lettering that is seen on the side of the hijacked 747 was blue and quite large. But in reality in 1986 the Pan Am 747 fleet had the titles smaller and in black.
Neerja held a conversation with radio engineer Emran Ali before the terrorists stormed into the plane and the flight attendants could not prevent them in time. Neerja thus informed "hijack" to the captain via intercom. In fact, Neerja, who stood at the door greeting boarding passengers, rushed towards the intercom. She shouted out the code number used to warn other crew members of a hijacking when she had her hair grabbed by one of the hijackers, which was overheard by another stewardess (Sunshine Vesuwala) who immediately informed the captain.
The person who is shot dead first is introduced to the flight attendant by his grandmother as 'Rahul'. Actually his name was 'Rajesh Kumar'. Factually the movie got other parts of his character right: he was an American citizen of Indian descent and was traveling to the U.S with his grandmother and aunt.
In one shot in 1985 with Neerja and her family having food at 1:23:10, bottles of Kissan tomato sauce and Del Monte are seen, but that label and those bottles didn't exist at the time.
When the 747's name "Clipper Empress Of The Seas" is seen it is in a completely different font to how it was on the actual 747 in 1986.
British passenger Ronnie Heston was caught by the terrorists with a burgundy-colored UK passport. Burgundy-colored passports were not issued until 1988.
When one of the terrorists shoots the radio-operator inside the cockpit, a crew member can be seen in the lower part of the screen, on the ground of the cabin.
Some terrorists have beards but no mustaches, a sign of a religious man but no terrorist in the actual incident had such beards.