Hi Peter,
I noticed on that site that if I start on one page and click a link to another the page continues to contain an HTML element that says the canonical link of the new page is actually the old page.
But when I navigate to a new page the canonical link keeps pointing to the old page:
Hypothesis respects canonical links. When you annotate on a page and we see a canonical link that doesn't match the URL we perform what we call
document equivalence. At this time there's no way to reverse document equivalence, unfortunately. My best guess is that something similar happened to someone on your problem page; someone had navigated there some another page, annotated, and then we made the two different URLs equivalent to one another.
We also serve up annotations based on the canonical URL, so you're going to see those annotations over any page that has the URL the annotations are associated with as a canonical link.
I'm sorry I can't be more help. Please feel free to send any questions my way.
Best,
Michael