The Internet’s Dr. Drang:
The idea behind the popular page is that it counts up repeated bookmarking of the same page. Pages that have been recently bookmarked by many users show up on the popular page, presented as a single entry with a count. The eulogy shows up repeatedly because Pinboard collects links according to their URLs, and the Times doesn’t have a single canonical URL for that page. When you’re on a Times page, the URL in your browser’s toolbar depends on how you got there.
This is a tricky problem. Last year I had a fun internet project idea basically destroyed at its earliest prototype stage because I couldn’t figure out how to do canonical URLs for a given web resource and without them my entire idea basically fell apart.