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arjaybe, most word processors manage to leave behind various bits of detritus. Most of it is tends to be fairly harmless, a result of repeated editing. Things like emphasised spaces and other such formatting that does nothing. For obsessive people, like myself, that look at the source, these things are an eyesore (but not much worse). Every now and then something else gets left behind that may not be visible in the word processor but may upset an ereader (empty columns or other such stuff). There can also be artefacts from the conversion process itself, which is rarely perfect. A lot of that sort of stuff has more to do with how careful you have been with the use of styles while creating and editing your text, and it's difficult to be completely consistent (especially with how most editors work) over the life of a manuscript.
The other thing about a visible table of contents is: how much does it really matter if it's there? Kindle automatically takes the reader to the start of the text (if you've set that up correctly), and for everyone else it's a matter of a swipe or button press to get past it. (It reminds me a little of the big deal that used to be made over how many clicks it took to shutdown Windows ... I mean, really, what did it matter if it was one click or two?)
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