I am not persuaded by your simple human argument, you know what I’m sayin’?
All “is, is” phrases get under my skin.
A colleague of mine says “I kid you not” about 10 times a day. Or so it seems.
“The thing is . . .” Urgh! One of my bosses must say this 50 times a day, and our office is small and she speaks very loudly, so it’s hard to ignore. And it literally never has any relevance to what she’s saying. “I know, right?” is another one she uses.
Another one - “. . . on the same page.” A church leader at my old church used to say this multiple times during any of her speeches.
Not spoken, but there is a poster on here that starts half of his sentences with “BTW.” But his posts are somewhat controversial and highly entertaining, so I will keep reading them while at the same time being annoyed.
That construction is simply wrong, but you can run into a similar problem using focusing statements and cleft sentences that feels harder to correct.
“What it is is a discrepancy between the audit trail and…” Deleting the is doesn’t fix it and reorganizing the structure of the sentence is more work than most speakers seem to want to do. Usually it’s not very noticeable in speech.