In Star Trek II: The Wrath of Khan, a female officer, Lt. Saavik, is frequently addressed as "Mister Saavik". It is claimed that this follows some real-life military (in particular, US Navy) tradition (Source 1, Source 2, Source 3):
In the US Navy the rank of an officer determines how they may be addressed in certain situations - Ensigns, Lieutenants (and JG Lts) may be addressed as "Mister -----", regardless of gender. Recognition of the rank earned, the role and not the gender.
Well, I gotta tell ya shipmates I must disagree with some of the above due to personal experience, and I have served in many commands with many officers both male and female. In my entire U.S. Navy career of almost 20 years, I never heard a female officer refered to as "Mister." I heard many male officers refered to as such but never a female. And it wasn't just Lieutenants, it was any non-flag rank officer.