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caliber should not be creating ToC with ..... <page number>. Is it possible that there is already a ToC in the file and that caliber only convert it?
If you want sub-section, you probably want to edit your source html to useh3, h4 and so forth. calibre can only convert to three levels of toc so you might have to use Sigil to edit the ToC in the resulting ePub instead of having calibre convert everything.
That's my experience with it anyways, your millage may vary.
Best
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