The 737 that has the emergency situation toward the end of the film changes between a Boeing 747 and a Boeing 737 several times when shown from the outside.
The doomed Flight 290 was inbound to Chicago's O'Hare airport and was cleared for emergency landing on runway 19R. Later, when Jack Harris is watching the news report covering the crash-site, the reporter (voice-over) announces the crash happened "...shortly after take-off."
During the time that the computers and radios are not working,
a shot of the control room is shown with the screens and indicator lights operational. The next time the control room is shown, everything is off again.
In the opening of the movie when Transair 290 is shown flying it's clear that's the airplane is Boeing 747 (engines under the wings). Later, when crash site is shown, the debris are from a plane with an engine in the tail, like L-1011.
When the tower controller freaks out in horror that the localizer went down, the technician rushes on foot to a radar dish, finds a big dead bird, removes it, nudges the dish with his shoulder and gets it rotating again. The localizer (aka ILS) is a static array of antennae installed by the threshold of the runway.
When the incoming jet loses power to its radios the pilots then use their cell phones to contact the tower. However, cell phones do NOT work in airliners cruising at altitude. Even if they are very low the speed of the jet means that the cell phone can not connect because it will be passing through the individual cell towers so quickly that they will not even have time for the electronic "handshake" that is required to pass the cellphone signal from one tower to the next. Also the aluminum aircraft acts as a Faraday shield so any cell phone signal would be greatly attenuated.
The only way cell phones can work is in some of the newer airliners when the airplane itself essentially has a "cell tower" which can then relay the signals to a satellite and then to the ground.
While a golf ball hit at normal velocity would possibly crack a vehicle's laminated glass windshield, it would not have enough velocity to embed itself into the glass as shown.
The captain of the last plane to land has a "meaningful" conversation with his co-pilot, while pretending to do some work around the cockpit after pulling up to the gate. He reaches forward to his instrument panel and with a flick of a switch turns the engines off.
A jet engine can be shut off by pulling the fuel shutoff lever which is normally located under the throttle levers, which would be in the center console, between the captain and co-pilot.
"Doctor Shamaal Buckhargee, M.D., licensed pilot" calls the tower and they ask him to turn on his transponder at which point the controller room freaks out because another plane magically appears on the radar.
A radar can always detect a plane in the air so the controller would have seen the plane no matter. The transponder merely provides additional information for the radar computer system to display on the screen, such as altitude. So turning a transponder on or off cannot affect the visibility of a plane on a radar screen.
Jack directs a plane to descend and maintain Flight Level six zero zero zero. Flight Levels are only used above 18,000 feet. He should have directed him to "six thousand" instead of using a Flight Level.