You know the way Mastodon works means not everybody is guaranteed to see all of the replies (or even the same subset of replies) to any particular post? When people are on different instances with different federation policies responses are commonly not visible. Even when you aren't hitting federation polices and blocklists, your instance won't have all replies to a post anyway, if there are replies from people who are not followed by anyone on your instance.
You just need to deal with sometimes seeing people reply to things that've already been replied to, that's the nature of the fediverse.