When leaving a native comment on the site the URL entered in the comment form was ignored. Clicking on the commenter's name just reloaded the post itself.
I had previously removed all commenting functionality from the theme, rather than just disabling it, so had to re-add it when I started working with webmentions. Because they were my only source of comments everything was coded with them in mind and I forgot to rework things when I re-enabled native commenting.
It's fixed now.