Is this the device/NCX/logical TOC? If so, my guess is either the top-level headings aren't set up as such, or Google's converter doesn't parse them when generating the TOC.
ETA: Just double-checked and headings I tagged as "Heading 1" in Docs did populate the logical TOC when downloaded as ePub. That said, it also pulled in a lot of pretty dodgy CSS, including color and fixed units for font sizes, both of which are pretty bad for books meant for sale.