Users have been reporting issues with missing reply notifications and missing replies for a while. It's not obvious if you're not paying close attention, so I think most people won't really notice. Try counting the number of replies versus the number of replies shown. It doesn't appear to be a spam-filter issue either as those replies are benign and still exist if you navigate to them via a profile.

Here's an example I just pulled up that's the second thread on my feed: https://twitter.com/LordCarsonEsq/status/1615134592222257155

There are six replies here. If you refresh enough, you can see a different subset of two replies, so that's probably not a spam-filter.