The way it's designed to operate is that it checks if the author of a webmention has already been listed so that there aren't duplicate entries but some sites, for whatever reason, don't send the author as just a name - they might also include the post title for example - meaning the author check fails.
In the past I have manually edited the author information via the backend but decided to semi-automate the process.
I added an extra box on the plugin settings page which allows me to enter name/url pairs (comma separated with each pair separated by a semi-colon) and code to check the author's domain against this list. If the URL exists in the list the author is automatically set to the corresponding item in the pair and duplicates are ignored.
If I no longer link to the Directory why even bother? Isn't it just a waste of time and effort? Maybe. I suppose it's the knowledge that it's still there but not working entirely as I would like.
If anyone still uses the Directory plugin and would like me to update the version on GitHub let me know.