I'm sure losing a game in OT to Penn State has a lot to do with it, as it should. When you are 5-1 while destroying all your opponents other than an OT loss to a top 20 team, it isn't a stretch to be ranked.
GA Southern was blown out in their loss. App State was as competitive as you could be in a loss. Georgia Southern should have lost to Texas State, won of the worst FBS teams in the country. Compare the two same opponents App State and Georgia Southern have played. On the road, App State beat Arkansas State by 4 possessions. At home, Georgia Southern beat the same team by 1 possession. At home, App State beat USA by 45. At home, Georgia Southern beat USA by 35.
Other than having played one more game (with an easier schedule), Georgia Southern does not come close to App in any measure.
Lets look at teams with similar records, look at their schedules, and see why you think Marshall should be ahead of them before even looking more in-depth at their wins, losses, and how they played each of those games:
Miami: 5-2 (67)
Utah State: 6-1 (111)
Fresno: 6-1 (91)
Texas Tech: 5-2 (38)
San Diego State: 6-1 (77)
Houston: 6-1 (123)
Virginia: 5-2 (43)
Cinci: 6-1 (102)
Buffalo: 7-1 (98)
App: 5-1 (133)
Marshall: 5-2 (119)
Why do you think Marshall deserves to be ahead of any of those teams?