The flight engineer is almost a non-entity. There have been cases of first officers getting promoted to captain with 15,000 hours with absolutely minimal time manipulating the flight controls of the airplane. These behavioral characteristics have been addressed at a recent flight safety conference by the Flight Safety Foundation in Tokyo, and have been documented for at least 25 years, by sources within the airlines and Western safety observers. For credibility's sake, we'll assume that there was one waypoint error. Third, KAL aircrews are not viewed in the best light by the rest of the flying community.
Captain screws up the entry of at least one INS waypoint.
The mistake is not detected until well into the flight. He happens to intrude Soviet airspace at about the same time that a USAF E3A is expected, and gets shot down. We have the obvious entry error, which most of the theories surrounding the incident seem to accept. Easier said than done. They certainly had enough information to determine the fact, assuming that they were following accepted crew practices.