The last issue is that all-in-one page (aio) has several duplicate IDs. Sections like "#bonus" are repeated in multiple lessons. So when everything is combined on the same page, those IDs are no longer unique. This means that if you click a later "bonus" link, you are sent to the first bonus section, for example. I'm not sure how important that is but we could make the section names unique across all lessons.
From https://github.com/UMCarpentries/intro-curriculum-r/pull/166#issue-804120643 by @MrFlick: