When Maniac complains about asteroid belts and/or nebulas (depending on the outcome of previous missions), the rank insignia badge on his left breast pocket is missing.
Hobbes appears much taller in the introduction cutscene (when Blair lands on the Victory) than he does in the rest of his appearances in the game's cutscenes.
Paladin is listed in the credits as "Maj. James 'Paladin' Taggart" (Maj. means Major). However during the game he is referred to as "General Taggart" and like Admiral Tolwyn he wears a cross-shaped rank insignia badge, indicating a high rank. He was only a Major in the first Wing Commander game, in Wing Commander II he has been promoted to Colonel.
When the player has to select a wingman before a mission, unlike the rest of the pilots, Flint doesn't move when the mouse cursor is held over her.
Despite the story being set in the year 2669, some of the characters wear WWII campaign medal ribbons on their uniforms.
A hand holding Blair's ankle is visible when Prince Thrakhath plunges his claw into him and lifts him up in the air (if the player refuses to beg for the mercy in the cutscene that follows if the player ejects in the final losing endgame mission)