Science fiction film or tv show where a plane was about to crash, and the plane was transferred somewhere? And the live people were removed and replaced with already dead people before it crashed.
Was it on The Twilight Zone maybe?
This would be Millennium (1989):
They are abducting people who will not be able to affect the future any further and replacing them with copies of those who would have died. Thus, the co-pilot's strange comment came because all the passengers had been replaced with pre-burned duplicates in preparation for the upcoming crash.
Kind of makes me think of The Langoliers (1995):
Most of the passengers on an airplane disappear, and the remainder land the plane in a mysteriously barren airport.
It also makes me think of an episode of the new BBC series Sherlock, "A scandal in Belgravia" (2012). In the episode Sherlock comes across top secret information revolving around a plane full of dead people for some government conspiracy.
This sounds a bit as the first plot in The Event (2010).
Sean boards a plane and pleads with the pilot, Leila's father Michael , not to crash it into the President's press conference in Miami. As the plane approaches the press conference site, it flies into a vortex in mid-air and vanishes.
Afterwards, the plane is found with everyone inside dead, except they mysteriously revive later.