There are numerous examples that span many seasons and all divisions of College Football.
In the FBS, teams can play twice in one season if both teams are selected to play each other in the conference championship game due to winning thei respective divisions (UCLA and Stanford in 2012). The two teams might also meet in a postseason bowl game (LSU and Alabama after the 2011 regular season). In the lower divisions, two teams that met during the regular season often meet in the geographically regionalized playoffs (Division II Grand Valley State and Saginaw Valley State in 2013).
There are even some conferences, such as the Division II GNAC that has so few members, they often play a home-and-home series among all of its member teams.
Meeting twice in one season in unusual, but not unheard of.
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