As the confusing title says.

If someone flags something for a some reason only perceived to them:
Ex: "[FLAG] File is either corrupted, broken, or otherwise does not work - about 8 hours ago"
But it's due to their machine not rendering the video, how do you flag the flagging as being improper?

That's the trick – you don't.

All flags are reviewed by Real People ^tm. Posts don't just get automatically deleted when they've been flagged.
If the approver reviewing the post does not experience the issue, they will likely unflag the post and message the original flagger to see what the problem was.

Considering how many of these posts I see it being 50/50 comment section how it works and doesn't work and nobody has any idea what to look for, I would rather it be flagged so that I have some level of notification to come and check things out.
Because the problem is that files aren't simple, even regular JPG file can have EXIF rotation and embedded color profiles which can cause it to look completely differend to someone else than it does to you depending on the software and hardware you are using. Same with GIF files, if you create something with 10ms delay, some users can see it correctly, but for most it changes into 100ms making the animation playback in extreme slowmotion.

There has been improvements over the years to avoid getting files that won't play for users to begin with which should lessen these things.