Either the "reader" is crap or it just makes a website out of your epub but does not understand the epub-toc file. You could try to insert a html toc in the epub and use that. But frankly I don't understand why you make a crappy app out of the epub. Just sell the epub, if that is what you want. Nobody who looks for a book does that through an appstore. And if your app is than not even half as good as any ereader app out there, why should someone want that?
And if it is just an ordinary epub, there is no reason to make an app out of it. I would understand that, if you made a html book with javascript that is not possible as an epub (like interactive fiction that tracks decisions).
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