Say I have a store on widgets and in that store I have blue widgets, green widgets, small widgets, big widgets.
So on my main page (not sitewide) I added links to all of the different kinds of widgets using their titles as the link text.
In doing so, my main page got filtered (not penalized).
Hope that clears it up. This is not about links to the homepage having the same anchor text or anything like that. It's simply about the actual text content on that page having too high a saturation of the widget keyword.