Did you use the
online validator or did you run it on your computer?
Anyway, since an ePUB is a special made zip file, you can inspect it by opening it for example with 7-zip. Just be careful not recreate the zip. You can do this, but you would need to know how.
Upon inspection, you can check if there are duplicate files... You could also open the ePUB in Sigil or the Calibre editor (part of the Calibre program). That would probably solve the issue at once.