I saw that too. I used to run my own HN RSS feed that was just a pass-thru to HN's RSS feed, but with the comments as the primary link. No matter how often my feed reader fetched, I routinely saw links show up on HN Daily or HN Blogs that my pass-thru feed hadn't captured.
Eventually I learned that hnrss has a flag to make the comments the primary link. I switched to that, and no more problem.
Eventually I learned that hnrss has a flag to make the comments the primary link. I switched to that, and no more problem.