After listening to it many times i find that it was a mixing error most likely. Shatner said mister but they snipped the audio track and it came out sounding exactly like 'sir'
Only question i now have is the error on the Blu-ray only or did the DVDs (and previous formats) have the same mistake.
I am going to grab a copy of the episode on DVD from my public library and listen and see. Perhaps it goes all the way back to 1968 and it was always a glitch.