South dakota st proved they were better than kstate on their home field. And watching that game i truly believe sdsu wins that game at minimum 4 times out of ten.
But thats the only example i can think of that actually happened.
However i bet there are a handful of teams in fbs that could consistently beat the abismal likes of teams like colorado and purdue of last year. Every conference has that one, maybe two, really REALLY bad team.
You even have FCS teams beating "better" Big 5 teams too, many since the App State vs Michigan game in 2007.
Georgia Southern over Florida
James Madison over Virginia Tech
ND State over KSU
etc...