In order to fix this here are some steps I would have applied If I find these kind of problem:
* Double-check that you have added the canonical tags to the correct pages and that the URLs in the tags are accurate. Goal of this is to double check that there are no issues with the URLs specified in the canonical tags.
* Implementation of the tags in the html. The canonical tag should be within the <head> section of your HTML document. Goal of this to is to check where you have pasted those tags.
* Resolve any crawl errors if they exist.
* Check if the non-primary URLs have indexation issues. Ensure either google have indexed these pages or not. Make sure to use no index in the case.
Sometimes it is better to wait instaed as your process may be under process.