According to the Mozilla Develloper Network docs on xhtml, the "charset" is an obsolete attribute in a link tag and should NOT be used. So use search and replace to remove the charset="UTF-8" from each link tag. Does that then allow it to pass epub3 epubcheck?
If not, please copy and paste the top 10 or so lines from the xhtml file (up to the body tag) so that we can see if the nesting of tags is correct.
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