Are you sure it’s not a caching issue? Have you tried calling the webmention.io API from some other place than Hugo? (for example from curl)
Because if you don’t run hugo with the --ignoreCache param, it will cache remote content “forever” (unless it’s stored in a tmpfs you clean regularly). So you could get a first batch of webmentions from the API, but this list would actually never be refetched from webmention.io for updates 
That’s typically the kind of situation that got me wondering about configurable cache TTL.