I had an unusual circumstance happen to me this week. I had earlier refereed a paper for a top journal. For the first draft, I recommended a fair number of changes, but I felt that if they were all made, publication would be appropriate. There was also another referee, who opined that the subject matter of the article was not important enough for the journal.
The authors revised the manuscript and resubmitted it. The associate editor sent it back to the same two referees. The other referee basically did not budge, still saying that it was not worth publishing. I, on the other hand, recommended moving forward with publication, provided the authors made one more change. It was something that I had mentioned in my first report as well, and it represents a genuine error that really needs to be fixed.
At this point, faced with conflicting reviews (and possibly after a request from the authors), the associated editor sent the paper out to a third reviewer. Just the other day, I got a communication from the editor that he had decided to accept the paper. Included were the current manuscript version, the authors' responses to my second report, and the positive report from the third referee.
What struck me was that the authors had not fixed the mistake that I had pointed out in my first two reports. The response in their resubmission letter to it seemed to have completely missed the point. I was puzzled about what to do at this point. Eventually, I decided to shoot off a letter to the associate editor, reminding him that the authors had not actually addressed my one remaining objection.
I'm still not sure whether this was an appropriate thing to do. I apologized in advance and said it might be none of my business in the letter. I do have a pretty good relationship with this associate editor; he sends me a lot of papers and had nominated me for a refereeing award. I guess that, apart from what opinions I hear here, I will find out what he think of my writing to him.