Unindexed pages canonical tag and 404

My un-indexed pages includes over 35,000 URLs. Bulk of URL issues are caused by “This includes Alternate page with proper canonical tag” and 404 URLs. How can I fix this?

I don’t think CS-Cart has default functionality to fix these issues.
Can anyone recommend solution or add-on to help fix this?

Extract the URLs from those reason you have mentioned and 1st check the canonical URL of them that mentioned. According to me, there will be a minor issue that need to fix in canonical URL then again submit for index.
And for 404 pages you can implement a custom 404 page and redirect them to respective page.