My bet is he is slightly injured. Havent heard anything about that tho... but with Chiellini out, is very strange to see Benatia benched.
Maybe allegri considers him out of form in some way?. But apart from his "blunders" who costed us points in the last games.. i have seen him in good form. So im not sure anymore of anything.
Still IIRC last time we played Rugani and Barzagli things didn't go well. Whether he made a mistake or not he has more to offer to the strength of our defense than both.