I usually only see that error when there are href attributes that are comprised of fragment identifiers with no filename (or something similar). I've seen it happen when doing a lot of splitting/merging in Sigil. Only I've never seen it in epubs that Flightcrew and/or EPUBCheck gives a clean bill of health. Usually ALL validators will bark at that sort of thing... not just some. Are you absolutely sure you're submitting the same file to Smashwords that you're validating with Sigil and the IDPF's online checker?
EDIT: See
if anything here helps.