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Sigil does create the container file automatically when creating a new epub. And I can't imagine it (Sigil) allowing you to open/edit an existing epub without one. It belongs in the META-INF folder of the epub (which Sigil doesn't allow you to edit).
Are you sure you haven't manually unzipped/edited and improperly rezipped the epubs (outside of Sigil) in question before attempting to upload them? Epubs aren't just regular zipfiles with a renamed file-extension.
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