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.
He played basketball for the University of Michigan from 1940 to 1943. He was the team's leading scorer for two consecutive years and set the school's single season scoring record with 230 points during the 1941-42 season.
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Avery Johnson
The UNC men's basketball team went 8-20 during the 2001-2002 season.
A college football player can be red shirted any time during the season unless he has played a single snap in any game in that specific season.
Wilt Chamberlain played in 1,045 regular season games and 160 playoff games and did not foul out of a single game.
Rutgers
258. Courtesy of the college of Troy.
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David robinsonI
1982 Wichita State Shockers were 73-14 and established an NCAA record for single-season wins
Cheryl Miller