Jeremy, I think this was a known issue with the WordPress Semantic Linkbacks pluin and thought it got address/fixed in a recent update. If not, do file a bug at https://github.com/pfefferle/wordpress-semantic-linkbacks
Also interesting, it looks like Independent Publisher (theme) isn’t outputting a permalink for the comments on Among The Stones either. If they’re webmentions, all the URLs point to the locations of of comment originals, which makes it harder to target individual comments with fragmentions.