It makes sense to check several things about your canonical tags, including whether some links currently pointing to non-canonical versions of your pages (i.e., duplicate non-primary versions) could point to the canonical version instead. Start by getting an inventory of your canonical tag implementation.

To find non-canonical pages (i.e., pages with a canonical tag pointing to another page) and the URLs they are linked from, navigate to the "Distribution of Canonicals" chart on the Canonicals tab of SiteCrawler's Content report:

Click on the Canonical Different section to view a URL Explorer report of pages with canonical tags pointing to other pages and the pages they point to.

Add the following columns for pages that contain links to these non-canonical URLs: "No. of Follow Inlinks" and "Sample of Inlinks":

The resulting report shows the list of non-canonical URLs with the number of pages they are linked from (through follow-type links) and a sample of URLs they are linked from.

You can export this report to have the full list of pages to correct. The Sample of Inlinks column shows the pages where you need to replace links to non-canonical pages (Full URL) with links to the canonical version of the page (Canonical To).