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Did you keep the old url in webmaster tools?  With sitemap of old domain that redirects?  You should make sure that was submitted for crawl so google see's the 301's.  Also make sure you redirected all versions http, https, www, etc of old domain* to new https//: version. Are the pages in fact 404 pages?  are they pages in your sitemap?  be careful too that they are not bad internal links.  Did you crawl site with moz?