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.
Yet the Shat stuff about Robert Sparr does lend credence to him throwing his weight around (no pun intended) in ways that weren't necessarily best for the show (and that from a longtime Shat defender.)