There's another scene that's always bothered me, but for the opposite reason.
At the very beginning of the first act of "The Cloud Minders," when Kirk and the landing party have been lassoed, Kirk has a line that's something like "Who are you? What is the meaning of this?" But his lips never move. I've never understood why the scene was edited this way - was there another take of Shatner actually delivering the line, but the director decided to use one in which he wasn't, for some reason? Or was the line looped in afterwards because it was decided that a shot of the landing party reacting without speaking looked strange?