The Premier League champions had an initial £28 million joint bid for the midfielder and left-back rejected and described as "derisory and insulting" by the Toffees.
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"I definitely do [sympathise with Roberto Martinez]," Moyes told reporters. "But I also know that if I was the Everton manager and Sir Alex [Ferguson] had come asking for Baines and Fellaini, I would have found it very difficult to keep them.
"I always felt the right thing to do was what was right for the players. All we can do is our job here. Roberto is in a new job and I am sure he will get to understand how Everton work. I know exactly how Everton work. I signed every player at Everton.
"I respect Everton greatly and I don’t want to do anything that would in turn affect them. Of course, taking their players would affect them but I am certainly only doing what I have to do in my job."