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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.