Cactus1805 I am not sure that I understand you correctly, but if I am, then this is by design.
References are not from one post to another, but rather from a discussion to another. Multiple references from a discussion to another will only create one back-reference event. This event does not point to a post in a discussion but to the discussion itself (URL without the "near" part).
What you are experiencing (one post marked as the source instead of another) is more what I am considering a flaw in Flarum itself, which is highlighting the first post of a discussion, even if no post is specifically targeted by the "near" part of the URL. IMO in this case Flarum should only open the discussion at the top without highlighting any post.
The back-reference event does not link to a specific post in the discussion because the idea of this extension is to mark that discussions have been linked at least once. Not to mark each time a discussion referenced another one. This is the way GitHub does it and I found it nice to use.