I'm not sure if this is a Lemmy issue, an instance issue or a Jerboa issue but occasionally when I hit the button to reply specifically to the main post and make a top-level comment, it instead replies to one of the already existing top level comments.

I don't know how long this has been happening; I only just now noticed it wasn't me accidentally clicking the wrong reply button when it happened twice in a row and I was making absolute sure I hit the right button the second time.