If Anae ran him every play I could see how it would negatively affect the offense.
But Carter gets the ball maybe 1, 2 times every quarter. He's never had more carries than any other RB this season. He gets put in to give the other backs a rest and maybe to run a play the newer backs aren't familiar with.
Focusing on Carter is scapegoating; he's a proxy for the overall frustration with the offense (which, incidentally, hasn't been bad except at Michigan).