My site structure is somewhat complicated and I've had a lot of issues with the rel=canonical pointing to a page that has different content, leading Google to ignore my canonical URLs. Currently Google is indexing the non-canonical pages, but they are usually outranked by a less relevant canonical URL.
The core problem is that for a URL that has multiple taxonomies, the canonical points back to the main category archive. ie. the canonical on "mydomain.com/category/category-slug/?tag=tag-slug" is always "mydomain.com/category/category-slug/". I don't know if this is the intended behavior for the plugin, but it does not work for me.
Is there to fix this so that the canonical URL doesn't remove tags or custom taxonomies from the URL?