[Quoth]

Conversion from PDF to ANYTHING is often doomed.
You need to use either HTML or DOCX and then Calibre or Sigel to convert.

As Hitch says, without more info we can't imagine the problem. There is also an online epub check run by the daisy group, who I think develop epub.

Is the complaint about TOC or content?

PDF is SOLELY a format for paper printing and perfect screen preview of the print job and defines an exact physical page size.

All ebook formats are independent of page size, being internally like HTML (or actually HTML + CSS) and not at all intended for paper. They are supposed to reflow on differing sized screens and also when font changes.

Comics may often be image based so are challenging to package up as ebooks except for larger ereader screens. Smashwords don't support any of the the specific comic / manga formats which are really wrappers on multiple images.
A PDF is also a wrapper, but can have postscript like text, vector images and bitmap images as well as layers per page. Unlike any ebook the page is a physical size and it's not meant to ever flow or resize content.

Use some other method to export your artwork than PDF.