Do you mean that your Moz Analytics Crawl Diagnostics Report is showing duplicate titles for pages that have rel=canonical? If so, this is something I noticed a few months ago & brought up to the Moz team. I believe it's something they're working to implement/somehow allow us to 'check off' pages in the report that we've already implemented a solution for. Also, if this is your situation, I think you should add your experience / request to Moz's feature request forum.
I hope this helps!
& I noticed that they have added rel=canonical site-wide (to prevent any unforeseen dup content issues). You can see an example of how it's used by viewing the source code here: