I don't see a subscribe link in this discussion :en:Wikipedia:Village pump (proposals)#Removing links to portals from the Main Page's top banner. There is a level 3 heading immediately after the level 2 heading, so maybe that's what's breaking the Notifications.
Topic on Talk:Talk pages project/Notifications/Flow
Great spot; thank you for reporting this, @Kyykaarme. This ticket now exists as an issue in Phabricator here: phab:T295200.