Marshall's Rakeem Cato had seven touchdown passes but threw four interceptions.
Doughty broke the previous conference record of six TD passes set on eight occasions.
Western Kentucky (7-5, 4-4) foiled Marshall's bid for the fourth perfect season in school history.
Marshall (11-1, 7-1) saw its 13-game home winning streak snapped and likely lost its chance to earn a place in the New Year's bowls.
Marshall already has qualified for next week's conference championship and will meet the winner of Saturday's game between Rice and Louisiana Tech.
