This is expected Google behavior. The Google documentation makes it clear there’s no promise that all your content will be indexed, no matter how many times you submit your sitemaps or individual URLs.
If you see any errors that may be attributed to Cloudflare, let us know what the error message was and perhaps someone in the community will have faced the similar error and may have a solution.
Can take time for Google to show all your content even when it is crawled. Have you logged into webmaster tools (nowadays called search console) to check the paths can be crawled.