That post was flagged away from the front page for some odd reason. The comments from that post would ideally be merged into this post.
I have noticed a number of interesting submissions with good discussion get flagged recently. I'm not sure if something changed with HN or a few users have gotten aggressive with that button.
Does anyone know if there is a way to vouch for a submission, like can be done with a flagged comment?
While @tpmx said flagged, there's no button for "flagged away from the front page" (unlike the story flag button). Dan has mentioned in the past poor quality comments and flame wars will cause a story to get down ranked, there's not a lot an individual can do (other than not fanning the flames).
What do you mean, "unlike the story flag button"? That is the primary mechanism used to move posts away from the frontpage when it upsets someone. This is not particularly controversial - I feel you might have misunderstood something.
The story was not flagged, even though you feel it shouldn't have fallen of the front page (moot now they're merged). A flagged story will disappear, but after that it's HN algos that decide what sits on the front page.