You are probably no-indexing some pages or category archives in the WordPress SEO settings, and then including them in the sitemap, when they should not be included. If that doesn't solve it, I would go to the sitemap settings for where the excluded robots.txt exclusions are and force it "never include." Or you can set the index to "always index" and include in sitemap. The two should work together - if something is in the sitemap, it should not be blocked by the robots.txt file. Also of note is that you can have a manual robots.txt file and also have other pages no-indexed by the WordPress SEO plugin that won't show in the robots.txt file on your server.
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