Though the movie takes place in 1988, the flag in the courtroom scene (behind Sheen) is a 48 star flag. As the court is an American court, it should have, it would have, a current 50 star flag, NOT a 48 star flag.
The year of the trial is supposed to be around 1973 (date of Sigrid Radke's coerced confession), but the film was shot in contemporary Germany. In a street scene, Gunther X (Sean Penn) walks by a Berlin electronic shop advertising compact disk players (introduced in the early 1980's). Also, Judge Stern refers to the Nurenburg Trials as having occurred "45 years ago", which would refer to the present as around 1990.
Martin Sheen arrives in Berlin on Pan Am Clipper Intrepid in late 1978. The aircraft was sold to another airline in 1967. Other airframes with the same name were present at the time, but none were single-deck four-engined aircraft.