As a result, you have some scenes in season one where you can clearly see crew members in the background; some shots of the end of the set (where a wall just ends for no reason); and I think that there are also a couple of boom mikes that creep in.
John Flinn absolutely knew he was filming widescreen. The cameras were marked for both fullscreen and widescreen. You can see this in one of the early documentaries (the one hosted by Walter Koenig). Such shots don't exist as far as I know. Stuff like the painting at the end of the central corridor was visible in either version.