Canonical URL's on my NextGEN gallery site cause large numbers of unique pages to be marked as non-indexable. My site must therefore run with canonical URLs OFF.
Unfortunately WordPress SEO turns canonical URLs ON and unlike other SEO plugins does not (appear) to have an ON/OFF option. I see other entries in the forums where people have removed the WordPress SEO code segment managing canonical URLs so it appears this type of problem does impact other users.
I would therefore like to suggest that perhaps this functionality can be added at a later release.
A more complete description can be found at Yoast SEO and NextGen Canonical Issue.