Take the simple case of a Flow page with a single topic and just its original comment. At the bottom of the page, there is a small/faint "Reply" link, and then below it is a large/prominent "Reply to xxx" box. At least twice, I have been lured in by the big box, and only after hitting the big green Reply button to submit it, I have realized that I should have actually pressed the stealth Reply link.
The result is that people who meant to reply to a specific comment are often going to create a new top-level comment for that topic.
I think the two replies should be equally emphasized, and/or should be much more clearly labeled, so the user can make an informed decision, and hopefully can choose the right one.