The slip-up occurs throughout the movie. In the cockpit of an F14 there is NOT a stick in the backseat. Throughout the movie they have the person in the back seat as "having control of the stick".
In F-14's there is a stick in the rear cockpit for the radar intercept officer to use. No, it does not control the aircraft, but rather the radar and weapons systems. It may have confused some people who are either not pilots or not familiar with the F-14. I am both.
Are you sure you were watching the same movie as me? At no time did the back seater have control of the aircraft. The pilot was always seated in the front, which is the correct position.