There are some configurations that may be affecting this:
-
suppress reply directly above
Don’t show the expandable in-reply-to on a post when there is only a single reply directly above this post. -
suppress reply when quoting
Don’t show the expandable in-reply-to on a post when post quotes reply.
They are all enabled by default to not clutter the UI.
Does the reply you’re experiencing this issue fall into one of those two situations?