@adoran2 It sounds like some of the issue might stem from your not having or using the Semantic Linkbacks plugin which helps to do a better job of displaying Webmentions as native comments.

Alternately (or in addition to this) some themes custom write "walkers" or other custom code to output their comments section instead of relying on the default comments output. These can cause display problems because they don't know what webmentions are, don't expect them, and therefor don't know what to do with them. Fortunately these themes tend to be few and far between these days. In my experience it's rare to run across these, but they can happen.

Independent Publisher was one of the first to do some custom work toward outputting Webmentions in a different way, but the developer did about half of the work and then stopped maintaining it. The two webmention plugins have since evolved to do more of that work. A slightly better maintained version of Independent Publisher by David Shanske can be found here: indieweb.org/Independe...

In general, the two plugins attempt to do most of the output work for displaying incoming Webmentions properly/logically, so you shouldn't see too many problems on the output side. However themes can override bits which can cause trouble.

The bigger problem with respect to themes generally is in the sending side since they may not have the best microformats mark up. As a result, when the receiving site gets a notification and parses the page, it either doesn't find the expected data or displays other data instead. In some of these cases you may want to manually go into your comments admin and tweak these manually. These don't happen frequently in my experience, though occasionally I will need to go into the admin settings and change a "mention" into a "reply" so that it shows the actual content I expect instead of saying that someone mentioned a post.

More details and subtleties on these: indieweb.org/WordPress...

If you have particular questions or need some help, stop by the chat: chat.indieweb.org/wordpress...