That's because it was not submitted when you think it was. The submission came here via the second-chance pool. That means that it was submitted recently, in this case yesterday. It might have gotten a few points and comments at best but did not really catch on. It was deemed interesting enough and moved to the second-chance pool to be automatically put on the frontpage a few hours later again. The process rewrites timestamps as far as I know. You can see it in the list at time of writing this:
I see a number of subthreads that were all posted 40-41 minutes ago, some with longer comments in them which might be the ones you have noticed. I would bet that these comments were posted before the submission was lifted to the frontpage for a second time. Consequently their timestamps were fudged so that they do not appear to have been posted before the submission time.
If you really care, you might want to ask dang (email hn@ycombinator.com) but I am confident that my explanation is not that far off.
https://news.ycombinator.com/pool
(You can also access the second-chance pool via the link labelled "Lists" in the footer of the front page if you do not want to remember it.)