Looking through the nodes in The Monastery Gates, it appears that “replies” is being used in the narrow sense of direct (immediate) replies to the OP, so that replies to those replies, etc., are not counted. For example, in the thread regex issue, there are direct replies to the OP by Anonymous Monk, AnomalousMonk, and Laurent_R, and these are the “3 replies” identified in The Monastery Gates.
I would guess that the point of listing a reply count here is primarily to draw attention to posts with no replies. In any case, I don’t think it’s a bug.
Hope that helps,