"Star Trek II: The Wrath of Khan" : Mistakes and Errors

It is unclear exactly how Saavik can be both a Starfleet cadet and hold the rank of lieutenant, unless she was had already graduated from the Academy and was now attending command college.
Incorrectly Regarded as a Mistake: The interior of the Botany Bay varies significantly from what was seen in TOS: "Space Seed."
This is not a mistake. In "Space Seed" the Botany Bay was left behind to drift away after Khan took control. In the movie, Khan refers to the structures the survivors live in as cargo bays that Kirk left for them when they were marooned.
The most publicized mistake of the movie is, of course, why Khan recognizes Chekov when the character wasn't introduced until the second season of the classic series. Several theorizes range from Chekov leading a security team to Engineering in "Space Seed" in a failed attempt to retake the Enterprise, to Walter Koenig's theory which claims that Chekov made Khan wait to use a restroom and depleted the stall's supply of toilet paper, at which point Khan exclaimed "I'll never forget your face!"
It is not explained exactly why Scotty brings Preston's charred body to the bridge following the battle with Khan. He may have lived had Scotty gone directly to sick-bay.
Kirstie Alley (Saavik) is visibly startled when William Shatner (Kirk) punches through the glass cover of the storage container aboard Regula I.
While Chekov is laying unconscious in the corridor adjacent to the Genesis cave prior to the landing party beaming up to the Enterprise, when the team materializes in the transporter room, Chekov has suddenly joined the group.
When the Reliant fires the torpedo at the Enterprise to prevent them from entering the Mutara Nebula, David is seen walking around Dr. McCoy's office, only to step off the turbolift onto the bridge mere moments later.
When the Enterprise jumps to warp to escape the detonation of the Genesis Device, the warp effect is different than in the scene where Sulu says "So much for the little training cruise." This is the result of the use of stock footage from "Star Trek: The Motion Picture" being used in the latter scene.