Sharing a recent areticle from +Pete Meyers on rel=canonical and adding some insight.

Point #10 Are Non-Canonical Pages Indexed?
For all practical purposes – no. If Google honors a rel=canonical tag, then the non-canonical page is not eligible for ranking. It will not have a unique cached copy, and it will not appear in the public index via a “site:” search. Now, does Google maintain a record of the non-canonical URL? I assume they do. As an SEO, though, the non-canonical URL ceases to exist in any meaningful way.

Google seems to diminish the weight of the canonical if you have cases where it has been misapplied. Example: product page 1 is replaced by a new updated page 2 with nearly the same content. Each page is kept live and has a canonical pointing to itself. You're created conflicting canonical tags for essentially the same content. Since Google cannot tell which page should be indexed, it indexes both and neither will perform well. For this to occur, it needs to happen in scale however, random errors are likely not a huge concern.  

If there are a high number of errors in a specific directory, it appears that Google is smart enough to isolate diminishing the value of the canonical to that directory so properly implemented directories perform as designed.   
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