Some pages have the {{noexternallanglinks}} magic word, which prevents sitelinks from Wikidata from appearing as interlanguage links. On such pages only the classic interlanguage links that appear in the page’s source are shown. This is especially common on main pages, which have a very long list of interlanguage links. Editors customize the list according to community consensus and usually show a shorter list of languages.
Applying both this kind of manual compacting and Compact Language Links leads to misleading results. As a simple first step to resolving this, CLL shouldn’t be applied on pages that have this magic word, under the assumption that the editors take care of the compacting. As a longer-term solution, the different use cases of this magic word should be examined and harmonized with the CLL behavior (T186470).