The Retired Emperor Gosaga appointed Emperor Kameyama's Prince (later called Emperor Gouda) as Crown Prince, instead of appointing Emperor Gofukakusa's Prince, and this caused a conflict between what it's called the Jimyo-in Imperial line (Emperor Gofukakusa's line) and the Daikaku-ji Imperial line (Emperor Kameyama's line) in later years, it also caused the big battle during the period of the Northern and Southern Courts (Japan) and even the post Southern Court.
後嵯峨上皇が、後深草天皇の皇子ではなく、亀山天皇の皇子（後の後宇多天皇）を皇太子にした事が、後の持明院統（後深草天皇の血統）と大覚寺統（亀山天皇の血統）の確執のきっかけとなり、それが南北朝時代、更には後南朝まで続く大乱の源となった。