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Are you trying to validate a file after uploading it to iTunes Connect? That error message is saying that the EPUB file you are trying to validate contains a file "iTunesMetadata.plist" which isn't listed in the .opf file. As far as I know, the "iTunesMetadata.plist" file is added to the EPUB file by the iTunes Connect software (I assume it contains metadata used by the iTunes Connect system).
What I'd suggest:
Make a copy of your EPUB file.
Working on the copy, change the extension to .zip.
Open the zip file and remove the "iTunesMetadata.plist" file from the zip archive.
Change the file extension back to .epub.
Now run that file through epubcheck.
The file should now pass epubcheck.
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