I think when some people tries to reply to someone, comment just becomes a reply to the main post instead of reply to the reply.
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ArgieGR8ArgieB8ArgieM8 [#2] test
It's only when you comment too fast and it says you need to wait 10 seconds. If you press "submit post" after 10 seconds it goes to the main thread instead. So yeah, you have to reload the page and press reply to that comment again.