The first step on the way to fix canonicalization issues is to find them. Here is what I do.
1. Go to www.google.com
2. Click on Advanced Search next to the text box.
3. Enter * in the "all these words" text box.
4. Select the drop down for Results per page and set it to 100 results.( the maximum).
5. In the "Search within a site or domain" enter your site name to be canonicalized.
6. Hit Advanced Search.
7. Once you get the results, browse to the bottom of the page and click on the link which says "repeat the search with the omitted results included."