I spotted an interesting Google Webmaster Help thread where a webmaster was asking why the most used words on his site is not showing up in the keywords report in Google Webmaster Tools. It seems like, at least for this report, Google may consider certain usage of a keyword to be over usage and would consider those keywords either boiler plate text or common words.

Jonathan Simon of Google said in that thread, and let me quote:

He goes on to explain that although it may not show up in the report, due to possible Google issues, this should not impact the site in a negative way. He said:

The question I have, is this not helping your site? I guess not.

Forum discussion at Google Webmaster Help.