Awhile back, a colleague and I wrote a paper and submitted it to a journal. The first round of reviews came back, and one reviewer told us our work was fatally flawed.
We went through a few rounds of back-and-forth with the editor, all the while repeating that Reviewer #7* was mistaken because of such-and-such reason.
Recently my colleague and I were examining our resubmission. My colleague drew a picture to clarify something, and I stopped dead in my tracks. "Holy crap, Colleague. Reviewer #7 is right! Our entire paper is irrevocably flawed."
We went though the data, checked a few things, and sure enough - fatal flaw. I'm not sure how I missed it the first time, I guess because I was not the first author and busy doing other things when we first submitted it.
So - 30 page paper goes in the trash. Clunk!
Now you might say, "But wait! Why can't you just fix that broken part? Write a big disclaimer within a limitations section?"
I can't fix it because it's wrong. The entire concept of the paper is flawed. Even with a disclaimer it would be disingenuous to publish this at all.
So I let it go. I'm not too sad, though. We actually re-designed how we'd do things to avoid this flaw in the future, and I am sure our next paper will be super fantastic when we write it. And in any case, there are always more great ideas out there.
(*) Not the Reviewer's actual number.