By default, the overlay shows clicks only for article-type links. The markers won't appear if:
the link leads to a category or a gallery page
the link is an article on some other website
the same link appears on the page twice or more. In this case, only one link will get a marker (that is located higher than the others)
the link leads to an article, but the URL differs from the one you have in page_url_canonical parameter in the markup on the page
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