Hi there!
It's definitely possible for a page to be correctly flagged as duplicate content while a canonical tag is applied. This typically happens in cases where the pages are being seen as duplicates of each other, but are canonicalized to different pages.
If you'd like to see a more specific example of where this is occurring on your site, I'd be happy to talk through it with you through a private message to help@moz.com :). I hope this helps to explain!
