Audio problem: When Kirk demands to know who the Troglytes are, his voice is dubbed over: his lips don't move at all. (00:04:05)
Audio problem: Just as Garth brings Spock back and releases Kirk from the cell, "inviting" them to dinner, there's an odd buzzing/rattling noise in the audio that shouldn't be there. (00:11:30)
Audio problem: In Zarabeth's cave, when McCoy says, "You've been dishonest with me, Spock," his lips are completely out of sync with his words. (00:42:00)
The Enterprise Incident - S3-E2
Audio problem: During the scene where Kirk is talking in the briefing room, the director was obviously not pleased with how James Doohan said his lines. Due to budget constraints, instead of re shooting the scene, they simply replaced Mr Scotts dialogue with another one. You can see it since at one point his lips are completely out of sync, even on the remastered edition. (00:06:40)
And the Children Shall Lead - S3-E4
Audio problem: When Spock asks Kirk, "Why are they bothering Starfleet?", there is a loud buzzing noise twice as they are focused on Kirk's face.
Audio problem: Spock uses the intercom to call Mr. Scott who is in engineering. As the shot cuts to a side view of Scotty standing at the controls, he answers "Scott here" but his mouth or lips never move. (00:44:24)
Audio problem: The bartender comes over and brings whiskey and five glasses, but we hear six glasses hit the table.
Audio problem: When Chekov goes berserk on the bridge, he emits a scream and shoves Spock. When Spock holds Chekov's face, the closeup on Chekov shows a scared look, and the original scream is played again, but Checkov's mouth doesn't match.
Answer: Kirk was getting his physical and Dr. McCoy probably turned off communications, because if he hadn't, Kirk would have left and headed straight for the bridge, leaving McCoy irritated.