Audio problem: When Uhura apologizes to Spock for interrupting him playing his instrument, her word is cut off mid speak between cuts. She says "I'm sorr-." But it's close enough it easily got past the editor or the editor cut her word off too soon not realizing. (00:09:59)
The Return of the Archons - S1-E22
Audio problem: In the transporter room, as Kirk is talking to Sulu, the door opens, McCoy comes in, and the door shuts. Trouble is that the characteristic sound of the door is missing.
The Man Trap - S1-E2
Audio problem: As Kirk low crawls behind some boulder and grass, his communicator flips open and closed. If it was opened, the sound of the channel opening should have been heard, but wasn't. (00:36:35)
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.