per @tabatkins:

Tab: If you're using <pre class=anchors>, that's very likely wrong. That's for providing all the info of an autolink, when a spec doesn't provide autolinks at all. There's a lot of copypasta using that, dating from when HTML wasn't marked up reasonably.

me: so, we're using both <pre class="link-defaults"> (some) and (mostly) <pre class=anchors>

Tab: Okay, so your "anchors" block is very likely completely unnecessary. Try removing it and seeing what still fails. If entire specs are missing, check if they're in Shepherd at all, or if I need to add them.

me: what if a term is <dfn>'d in multiple specs that are in Shepherd ?

Tab: That's just a normal ambiguous link, and <pre class="link-defaults"> can handle that to specify which spec you want it from. (Or you can do it at point-of-link with the spec attribute on the autolink.)