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Thanks Guys,

Turns out it was an indexing issue on the website. Magento was being slow to rebuild the index after seo friendly urls changed - this made it appear as though the canonical link on the page was pointing to the wrong place.

We've re-run the tool after manually rebuilding the index and all is good.

This might seem a bit of an odd one, but we seem to be going around in circles on this when using the on page optimizer tool.

We have an ecommerce site (magento) which by default is putting a canonical link in the header on every product page.

For example;

www.example.com/product1.html has the

But when we run the on page optimiser tool, we're losing points on the critical section for not having canonical set correctly.

If we remove the tag, we get the tick and the a grade, but then further down the report we lose a tick for not using canonical links.

What are we missing here?