The Blues boss was furious with the official for not stopping play when Steven Pienaar was down injured, allowing United's Danny Welbeck in to put the home side 2-1 to the good.
Jones previously brought the game to a halt when Jonny Evans needed treatment and Everton were on the front foot.
Moyes told Sky Sports: "I thought it was rubbish. He stopped play for Jonny Evans.
"The referees can do what they want, can't they? They really can. They can make their own mind up, make their own rules up. And I thought he made his own rules up today.
"Not to do the same on their goal - I don't know whether it was their second or third goal - when Steven Pienaar's down, you'd have thought then if he was being consistent that he'd maybe even it up, and say 'Oh, the player's down I'll do that.'
"He never did it and they scored from it. I've got to say I think the referee was poor today."