The production team first chose the Brazilian capital of Brasilia as the city in which to shoot the movie. However, because of logistical problems they ended up in Berlin, Germany, where they found most of their locations, such as a recently built crematorium, and underground sewers dating from before World War II.
Production was delayed for over a month while Charlize Theron recuperated from a neck injury she sustained while slipping during stunt training. After the injury she still insisted on doing her own stunts, although she does have a stunt doubles clause in her contracts.
According to director Karyn Kusama, after finishing the movie, the studio fired her, re-cut the movie to a 71 minute long version which tested poorly and then asked her to edit the film again, but not back to her original vision. Huge parts of the plot were left out and even one character's sexuality of being gay was cut out by the studio.
The trivia items below may give away important plot points.
For the second season of the original Æon Flux (1991) animated series, Aeon was killed at the end of each episode, only to appear alive and well at the beginning of the next. In the film, all the people in the world have died and been re-born over and over in a most subtle reference/adaptation of the original series.
The flower Cladius is handling when Aeon comes and confronts him about Una's death is a Rafflesia, and smells like rotten meat. Its local name translates into "corpse flower" and it is commonly found in southeast Asia. It is the official flower for Sabah, Malaysia.