This happened exactly once, in the 5:1 loss to Napoli. Before the world cup break, Fagioli barely played. Even his sub appearances were very limited. But once he got his first start, vs PSG, there was only one game where he was replaced by McKennie in the middle of the park, the game vs Napoli. He also didn't start the game vs Udinese, in which McKennie did start. But it was Miretti who replaced him in the middle of the park with McKennie playing as an RWB.
No idea why Fagioli didn't start or have many sub appearances in the beginning of the season, but I doubt age was the main criteria. Because at the same time Miretti started a bunch of games and a lot of sub appearances.