Visible crew/equipment: In the very beginning, the boom shadow is visible at the top of the screen as Kirk walks to Spock's station on the bridge. (00:00:30)
Visible crew/equipment: A camera shadow briefly intrudes on the right side of the screen as Kirk asks Mr. Scott about the sensor readings. (00:00:55)
Visible crew/equipment: After Uhura asks McCoy if she'll become like Chekov, McCoy reassures her about finding an antidote. Then, when it cuts to Engineering, there's an actor's black tape mark and a chalk T-mark visible on the floor. (00:38:10)
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.