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.
Plot hole: Gene's plot has far too many holes for it to have had any chance of working in real life. He somehow must get himself assigned to that particular flight (OK, maybe as a flight marshal he could persuade his superiors to assign him to it) - but also hope that the air stewardess Stephanie is also assigned to that flight - something he has no control over. He then needs to push Jodie Foster's husband off a building, hope the corpse is taken to the only morgue in the city with a crooked morgue director, hope the coffin is assigned to the flight he is on. On top of that, he needs to get explosives into a coffin, the combination of which he actually says he doesn't know. He also needs to hope no-one notices the child, the child doesn't make a noise while boarding, there are lots of spare seats on this inaugural flight, and that mother and daughter move to them.
Plot hole: Bomb squad vehicles are present at the airport when the plane lands. There is no bomb disposal unit in Goose. If one is needed it has to come from two provinces away - travel time by vehicle, in March, going flat out: minimum 20 hours + a 2.5 hr ferry trip. Not to mention that the markings on said vehicles are American: transportation of those vehicles from the US wouldn't have been any easier than from Canada, on the contrary, so again, they wouldn't have had the time to bring them over.
Plot hole: The premise of Carson framing Kyle is utterly ridiculous. Not only the fact that the authorities would never accept a ransom demand without speaking to a supposed hijacker, but Carson has absolutely no evidence to give that Kyle is a hijacker, and yet the FBI somehow all know who she and treat her as a hijacker just from her looking at them from the plane door. The movie seems to act as if an Air Marshal's word alone is enough to convince the authorities that a crime or hijacking is happening aboard.
Plot hole: Along with the $50 million, one of "Kyle's demands" from Carson is that the FBI provide "her" with a Gulfstream III plane, which is presumably which he plans to escape on. This is actually the stupidest mistake he might have made. If his plan had succeeded in framing Kyle and having her holding the detonator in her hand dead, he wouldn't just allowed to leave like that, mostly because with the threat over the plane would have been withdrawn. His $50 million might have been withdrawn too, if his account wasn't protected.
Plot hole: Carson states to the captain that Kyle is a "hijacker" and is threatening to blow up the plane unless they transfer $50 million to an account (which we don't see.) He also tells the captain that she refuses to negotiate, and to agree to the ransom without speaking to her. In the next scene, Carson receives a call from the captain that the money has been transferred. Law enforcement would never agree to a ransom demand without talking or knowing who the so-called hijacker is. When Kyle later looks outside the plane, she sees bomb squad and law enforcement treating her as the hijacker. There is no proof or evidence that Carson has given that Kyle is a hijacker, nor is there a background check or identity on her. Law enforcement would have never treated this so seriously as they did at the end, nor would bomb squad have had the time to make it, as mentioned in another mistake.
Plot hole: The hijackers somehow know who Kyle is, and what her job is, and what kind of family she has even though Kyle doesn't appear to have known them prior to meeting them on the plane. The only time she met the morgue director was at the beginning of the movie when she went to see her husband's body before deciding to board the plane, so there is no way they could have known who Kyle was, and that she had a husband, and an only child, for a whole host of reasons. Firstly, the information about passenger plane designers is protected by very tight security to keep people from having access to to it. Secondly, passenger plane designers are secretive people who don't speak publicity about their jobs. Thirdly, passenger plane designers rarely interact with Air Marshals, and flight attendants, as they all work in different places. These three reasons I mentioned are to keep people from learning about avionics engineers, and their families in order to prevent the exact thing the hijackers were the trying to do - framing an avionics engineer.