I don't know if it needs to be coded so that teams don't lose to FCS teams. Because anything can happen. I'm not saying it's likely to happen but it could happen.
Part of the problem with upsets is that too many teams are overrated. Therefore the lower teir teams are even with mid-to-top teir teams, causing an insane amount of upsets. But they actually aren't upsets because the ratings are soo close. For example and no offense to any fans out there but how is NCstate low 90s offense and high 80s defense, Same goes for Maryland, Ole Miss, Fresno State is rated as a 2 star and has a 85 overall team?? All teams have good players but not enough to consistently compete with top teir teams currently. EA admitted that they want everyone to enjoy playing with their team so they skew the ratings up. Which leads to too many evenly matched teams or mid to lower level teams with high enough ratings to beat top tier teams. The ripple effect is that when the once in every 2000000000 dynasties that FCS beats Oregon it looks like a pattern even though it is not.
Average teams should be between 75-83, above average teams should be between 84-87, really good to great teams 88-99. Currently average teams are around 85-87. That just too close and why we have so many crazy upsets.