Thats strange, it's happened to me before on a few videos, and I just assume the comment had been deleted by the user, or if it had been a long time since the comment had been made I just assumed that the actual account itself could have been deleted
I'm not really sure the specific reason, but especially on my bigger videos (like my top 3 most viewed videos) I have had quite a few comments go missing! some of them were butthurt comments, like someone trying to correct me on something I said in the video then realising that i was actually right, that comment disappeared within a few hours of it being posted haha