This must be deleted pages/pdfs that are still referenced in your post content. These will be detected as 404s when bots are crawling your content. If one error is very common then you can redirect this to the parent post or the homepage using the redirections module.
I am not quite sure where this modification is coming from but it must be stemming from one of your installed plugins or the theme.
I have also checked the other issue and your site was having a problem of loading the sitemap_index file. I have fixed this error but it does not seem like the search console is fetching the sitemap.
Could you please login to your search console and check if there are any coverage errors and whether the sitemap file links have been fetched?