Okay I have a random and weird fix that seems to work frequently for me. I generate my epubs in Calibre, then rename them to their isbn.epub name, then open them in Sigil, run a validation, and save it.
Just opening and saving in Sigil seems to get rid of some of the more random little errors that show up. Epubs for some reason hate it when you rename them, without opening them, then resaving them after. It should in theory not matter, but I think because its a zipped file it messes things up.
Anyway so I would suggest open in Sigil, save and re-run your validation.