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Yes, that file gets added to an ePub if you view it using iPad, iTouch, etc, or if you run it through the iTunes publishing application.
Simplest solution would be to change the .epub file extension to .zip, open the zip file, find and delete the iTunesMetadata.plist file from the zip archive, close the zip file, then rename the extension back to .epub.
If you want to view/check an ePub on an Apple device, best to make a copy of the ePub and view that, so that the original remains untouched and doesn't get that iTunesMetadata.plist file added to it.
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