Without actually looking at your epub file, I would only be guessing as to the cause of why code showing up. Have you tried to sideload it onto an actual device? if possible, you should always sideload and never fully trust what you see with the online previewers.
Two days ago, I uploaded a 193 kb EPUB that had been blessed by EPUBCHECK. Before I officially published my EPUB, I used Manuscript Editor just to look at the EPUB; I didn't change anything. When I clicked "PUBLISH," I first clicked the button that said "Use the file I uploaded" instead of "Use the book as changed by Manuscript Editor." But despite that, what was published was a 725 kb EPUB file with garbage in it. Today I wound up re-uploading the flawless 193 kb EPUB file, and now everything's fine. If you want to write for EPUB, then I suggest that you each download Calibre ebook-conversion software, and email each other revised HTML versions of your book. At least for now, Manuscript Editor is a snakepit.