Canonical warnings

[PatioLifeStyle]

[1] My site development tool (XSP) has recently added the canonical reference as an auto-generated tag, so every page of my site now has it. Why is SEOmoz warning me that I have hundreds of pages of canonicals if it's supposed to be a GOOD thing?

[2] Google is still seeing the pages without the canonical tag because that's how they were indexed. Will they eventually get purged from their index, or should I be proactive about that, and if so, how?

Thanks for any input.

[BrianCrouch]

Forgive this question: is the autogenerated canonical URL to the root domain or to the page-deep URL? I only ask because I've seen autogenerator tools set the incorrect canonical and checking to see if it's possible that happened on some of your pages.

[PatioLifeStyle]

Every page has its own rel=canonical link reference.