I vaguely recall this issue being well(?) known, but the Parsoid output requires a particular URL setup.
Given a URL of the form: http://localhost/.../mediawiki/index.php?title=Main_Page&variant=sr-ec (for instance) the legacy parser will generate full absolute URLs in its output, eg:
<a href="/.../mediawiki/index.php/Tricky_Question_Marks%3F/Subpath/Child" title="Tricky Question Marks?/Subpath/Child">Tricky Question Marks?/Subpath/Child</a>
however Parsoid generates relative URLs (./Foo) which resolve incorrectly when the base href is '/index.php' because the proper URL *should* be /index.php/Foo.
This is an issue when including Parsoid content on a page, as the base href for the entire page needs to match what Parsoid expects.