During preparation that might happen I guess, although it should not. If there is a margin between paragraphs, it could be interpreted as a section break. Those should be marked as a paragraph with as content [scbreak]. The [scbreak] is the default value and you can replace it by your own.
The reasoning for this is, that some use <p> </p> for a section break and others a margin. This would make it easy to find them.
Sometimes an existing empty paragraph around a header can get the same style as the header. Word is funny in that. That could lead to empty entries in the TOC, although I though I had worked around that. I will recheck that part of the code. In Word 2013 (and I believe also in Word 2010) you could quickly see that in the navigation pane. There would be empty headers then.
Like I said, I will double check that part of the code that would prevent this.