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I think you may be confusing an html toc actually appearing in the text with a toc.ncx which, to my limited understanding, provides navigation information but does not. It might be useful for you to open one of the short stories you downloaded in Calibre Viewer, and see what appears in the left pane under table of contents, which apparently reflects the contents of the toc.ncx. Or choose to edit the epub in calibre and see if there is a toc.ncx in that story.
I only replied to give you an idea of what the error was until hopefully someone more familiar with Scrivener and Smashwords responded. Since Smashwords submits to many Vendors it is subject to the quirks of them all. The error message suggests that some Vendors actually require a working toc.ncx with at least two entries. Seems a bit unnecessary for a short story, but I suppose the TOC can be a very simple one. You can easily create or edit a toc.ncx in Calibre using the editor and then the Table of Contents option, I think under tools.
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