The replies number that you see on the embedded topic list is derived from the same code as is used to set the replies count on the Discourse topic list, so possibly both issues need to be dealt with. I’m not sure if it intentional to include moderator action posts in the reply count on the Discourse topic list. Including moderator action posts in the reply count for embedded topics seems definitely wrong - especially since the first reply to all embedded topics is now a moderator post.
For examples of how moderator posts are included in the reply count in topic lists, have a look at this topic list: https://meta.discourse.org/?status=closed. The post that is created when a topic is closed is always counted as a reply. Maybe only regular posts should be counted.