I think the frequent problems we see with comments failing to nest properly can be fixed by changing the default behavior of the page that opens to read a particular post.
Right now, that page opens with big open “comment” entry box. It shouldn’t.
I think that a more intuitive approach is to require the user to click on SOME reply link in order get a place to type at all. Place the top-level reply button at the bottom of the thread-starter, before the comments. Maybe put another copy at the end of the comments, but clearly separated from the comments.
I wonder if this is the way the old BMG worked?
Meanwhile, it is still true that if a user opens a properly-nested comment, enters text, and then hits “reload” (before submitting the comment), it will be bumped to the top-level after the reload. This is a bug in the page reload code.
This is on the list of changes to be made. The old BMG platform did indeed require that one click on “reply” before a text entry dialog box opened. Separately, thanks for the bug report. Noted also.