I remember seeing an X-Files episode, one of my first series play-throughs I did in around 2008, where I clearly saw the boom operator to the right of Mulder and Scully, but I can't find any evidence online of it ever happening, but I'm 100% certain it happened.
I downloaded the series near the height of the torrenting craze (it took me a few days to download @ like 200 Kb/s), So I can't give you a specific box set year. I THINK that's where I saw it, but it may even have been on TV, but most likely it was the download.
The scene:
My memory of it is getting worse every time I try to recall it exactly, the mind is fickle and memories malleable, but this is how I remember it now...
Mulder and Scully have just got out of their requisitioned government vehicle and are talking while approaching a house. There are steps up to the house to the left, I think. The steps are like side-on to the front of the house (So you would walk up and turn right to face the front door). At the point where they are talking while approaching the steps, the camera follows and pans right too far and catches a short glimpse of the guy holding the mic boom. It's as clear as day if you notice it, but only a small part of the guy is visible.
That is my memory, but details of the scene may be wrong. It's the type of thing that when you notice, you want to tell everyone, so it sticks in your mind. I'm pretty good at spotting stuff. I just re-watched the entire series and spotted a few similar but less severe faux pas (I even spotted a "big", grown-up "boy-from-that-AI-film" in a miniseries episode that I was happy about. So I'm quite proud of my spotting and really want some confirmation that this actually happened, but most of all, I really want to see it again.
I'm guessing it would be an early episode, like season 1-3, but that's a logical guess. They probably would have edited it out at some point. The only scene that felt similar was "Eve" where they approach (I think) Cindy's house. But I have since found out (for reasons I won't go into), I missed some episodes this play-through.
I really hope this isn't the Mengele Effect.