The series was full of audio errors and clipped dialog. It often happened when looped dialog wasn't timed right, it gets cut off. They clipped the "Mis- from Mister most likely so Kirk's dialog didn't step on D'Amato's. The Doomsday Machine has some also, when Kirk is telling Uhura to have McCoy, Scotty, and a damage control party meet in the transporter room. "Mr. Scott" is cut off very quickly. Kras in Friday's Child has some bad ADR: "You and your primitive knives and weapons" always sounded like it was mashed up. The DVD/BR audio track "fixes" it, adding a "your" before "weapons." Which sounds just as awful and is now incorrectly on the "original broadcast mono track."
So, no, it was never meant to call him "Sir." It was an audio glitch from day one and has been like this since the original night of broadcast.