I was having this problem with Pages (on a Mac) documents exported as ePubs and then converted to Mobi in Calibre. I eventually found that if in Pages I made the text full justified then the words did not split at end of lines anymore on the Kindle. With a Mac, this seems to be the easiest way to get beautifully organized documents with a full TOC onto a Kindle:
1. In Pages create the document using Styles to set up the TOC where you want breaks (Heading 1, Heading 2, etc.) Use the Inspector to setup the TOC and which styles will be displayed in the TOC.
2. ***Make sure all paragraphs are full justified alignment. For some reason left-justified text shows up on the Kindle but words are split at end of lines. Full justification seems to fix this.
3. Export file as ePub.
4. Import into Calibre and convert to MOBI format.
5. Send to Kindle.