Quite a coincidence. I was just sent an epub which I decided to look at in Sigil. Sigil complained with an error message: "Files exist in epub that are not listed in the manifest, they will be ignored." I clicked on the Details button and read simply: OEBPS/cover.xhtml. The first time I've ever seen this message.
I renamed the epub as a zip and opened it in an archive manager. I found the cover.xhtml file in the OEBPS folder but it had failed to be referenced in the manifest although it was in the guide section. I typed in a reference, saved it and renamed to epub. Sigil opened it without complaining.
The epub had been created with Vellum for a "Generic" target. The CSS in the styles sheet seems terribly complex. Every chapter heading is wrapped in 6 <div> tags. Every paragraph has multiple class attributes and when I check what some of them do, they appear to have no effect at all.