John Malkovich was unhappy during production because the script was being rewritten virtually every day and he had no idea how his character was going to turn out.
The film is dedicated to Phil Swartz, an effects specialist who died during filming, when a rigged plane fell and crushed him. This is actually the second Jerry Bruckheimer production where there was a plane related death on set. Eleven years earlier, Art Scholl, a pilot/cameraman, died during filming of Top Gun (1986) when his camera plane failed to recover from a spin and plunged into the Pacific Ocean.
The Las Vegas scenes were filmed at the legendary Sands Hotel immediately prior to its demolition in late 1996. When the production team heard about the city's intentions to raze the historic landmark, they immediately scheduled a multiple camera setup to take advantage of the rare event, which is what you actually see in the movie.
The success of Con Air had subsequently changed John Malkovich's profile in Hollywood. While he was once typecast as the highly intelligent seducer, he was now first considered for the part of the highly intelligent criminal. Soon, though, those parts became unappealing to him, and Malkovich gravitated toward European productions.