I didn't know they continued after dark on location for "Shore Leave," using stage lights to simulate daylight. I'll bet those are scenes where the non-sunlight quality led me to think they had shot additional scenes indoors.
There are some shots by Lazarus's little ship in "The Alternative Factor" that look very indoor; now I wonder if they were just out there at night with the studio lamps on.
Also, Bruce Mars adds some evidence to the theory that William Shatner was a nice, normal lead actor, and the whole supporting cast animosity legend was cooked up after the series, behind his back.