Plot hole: The whole concept of a kidnapper 'pretending' his victim didn't get on the plane in the first place is utterly laughable. Even if nobody saw her in her seat, why didn't they see her walking down the aisle to her seat, or waiting to board the plane, or in the boarding tunnel itself? Why isn't she listed on the passenger manifest, or on her mother's travel documents or airline ticket? And there would have been security cameras all over the airport.

Flightplan (2005)
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Directed by: Robert Schwentke
Starring: Sean Bean, Jodie Foster, Peter Sarsgaard, Kate Beahan
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Flightplan stars Jodie Foster as a grieving widow and airplane engineer who boards a massive plane in Berlin along with her young daughter to take her deceased husband back to the U.S.A. What follows is a parental nightmare as, not only does her daughter disappear, but strangely no-one seems to have noticed the child and evidence suggests that she either doesn't exist or died. The mother's desperate search and infuriation at the mounting accusations that she might be insane lead to her being detained by an Air Marshall while alienating her from the flight crew and passengers. The plot gets even more convoluted and improbable, involving conspiracy, a ransom, hijacking and things best left for a Die Hard film. While Jodi Foster plays a thoroughly distressed but determined mother well, the rest of the characters seem half-realised and mostly just serve as plot devices. As the film nears the conclusion and the pieces of the dramatic puzzle fall into place, plot holes and utterly silly factual errors glare brighter than the runway lights on the Tarmac. OK for a Thriller/Mystery but a better written story with some attention to detail could have elevated this story to greater heights instead of leaving it circling on the runway.
Trivia: The role of Kyle was originally written for a male character, but when Jodie Foster expressed interest, the filmmakers felt she was strong enough to carry the part and cast her instead.
Question: At the end of the movie, when they are at the tip of the plane, Jodi and her daughter slip into a tiny compartment, just as she activates the bomb. She and her daughter are safe, and the small space they were in must have been bomb-proof. Since that compartment is at a part of the plane that is rarely visited, how come a tiny place was made entirely bomb-proof? Or what was the space they climbed into and for what reason was it made?
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Answer: The hatch they climb into is the hold of the plane, i.e., the section with the coffin, the car, and all the other luggage in. It only appears small because of the way it is filmed. As Kyle would have known, it would have been extra strong and reinforced, as it was a break in two sections of the plane.