I just want to know...is it caused by off-page factors too?
There are a lot of mistakes you can make when trying to optimize your site for your target terms, and keyword stuffing is just the beginning. Common traps people fall into that can make your site unpleasant for users and unacceptable for search engines.
to Google and the other search engines it makes no difference if a site is intentionally over-optimized to cheat them or over-optimization is the result of good intentions, so no matter what your motives are, always try to keep to reasonable practices and remember that do not overstep the line