Problem with Rel Canonical
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Background: We check to make sure that IF you use canonical URL tags, it points to the right page. If the canonical tag points to a different URL, engines will not count this page as the reference resource and thus, it won't have an opportunity to rank. If you've not made this page the rel=canonical target, change the reference to this URL. NOTE: For pages not employing canonical URL tags, this factor does not apply.
Clearly I am doing something wrong here, how do I check my various pages to see where the problem lies and how do I go about fixing it?
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You should check your rel canonical in the header of your html, and see where it's pointing to. Sounds like it's pointing to a different page. You can check this with the mozbar - analze the page, and go to the page attributes section - it'll show you the rel canonical tag for the page.
Send an example of the page if you want us to look at it and see if we can give you more specifics.
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This is a warning in our system that often confuses people, and we're actually looking to rewrite it. In many cases, a canonical tag SHOULD point to a different URL. By their very nature, many canonical tags are on the non-canonical version of the URL. We just warn people in case they made a mistake and created a mis-match they didn't intend to.
Since this is more of a support question, feel free to contact me through the Private Message system with the URL(s) in question, and I'll take a look.