Not sure I can explain this well, but I just saw a reply to a comment of mine in the inbox. When I click on it, it shows the reply to my comment, but if I scroll up, my comment is shown as a reply to a totally different comment to the one I originally replied to.

If I click to ‘view all’ button in the inbox, I can find my comment, and the reply that was in my inbox, and they’re all ‘threaded’ correctly.

Let me know if I can provide links / screenshots to try to share what’s happening.

Edit: when viewing the thread from the inbox, I also see lots of ‘More replies…’ buttons that don’t do anything.