The average time on site is calculated by subtracting the time between page views on your site. Therefore, if a visitor opened a page and left without navigating to another of your pages, there is no second view and therefore the average time is recorded as 0.00, even though they may have been there for minutes reading your page.
Of course, you would still like visitors to be clicking around your site for hours, but the average site time can be misleading, so bare this in mind.