Hi Tej,
Thanks for writing us on this! So Sheena and Karl are both correct. Although, an REL Canonical may solve the issue with Google it is still technically a duplicate title tag. When designing the tool we found that having the crawler pick up the REL Canonicals can be problematic for a coding and SEO standpoint. It is often possible that an REL Canonical will be directed to an incorrect page and since our crawler is so literal it would have issues recognizing the canonical was bad.
Our product staff is aware of this and they hope to get to a place where we provide an ignore feature, so if you feel that the tag was implemented correctly you can select ignore and we will no longer report that issue for that page.
I know that this is not ideal for many customers, but hopefully our solution will be comprehensive enough to encapsulate many of the solutions SEO's have found for these issues.
Hopefully this helps and if you have any other questions or concerns let me know.
Have a great day!