Fellaini was booed off the field when substituted during the Toffees' humiliating 3-0 FA Cup quarter-final home defeat to Wigan last Saturday, and appeared to confront angry fans as he left the field.
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“I won’t have any trouble picking him - I’ll play Marouane against City because I have to give the club and the team the best chance of winning the game, and that will mean picking our best players, and giving them the chance to go out and make amends," he told the Liverpool Echo.
“I have spoken to him. We have looked at the game, studied it and he knows that he should have played much better. His reaction to that wasn’t the correct one and I’ve told him about it.
“Yes, he may have some making up to do to the fans, but you have to also look at the good stuff he has done for us this season.
“For the most part he has been outstanding and made a massive contribution. It wasn’t right (his reaction) but don’t forget all the good stuff he’s done. He has played a big part in our season.
“Most people had a really disappointing day, he found it tougher than most. His general play on the day wasn’t great and he was frustrated.”
When questioned over Fellaini's dip in form, Moyes replied: “I don’t think you can go through an entire season playing in scintillating form.
“He may not be firing as he might but he’s still been influential for us. He is the only player I’m talking about but there were seven or eight others who we could equally be talking about. It would be wrong to single him out.”