Manager Moyes, who left Everton at the end of last season, had a £28 million (Dh160m) joint bid for the duo rejected earlier this week, which the Merseyside club branded "derisory and insulting".
Moyes's successor at Goodison Park, Roberto Martinez, questioned the timing of the offer, but Moyes says he remains on good terms with the club and their chairman, Bill Kenwright.
"There's a mixed market at the moment. Nobody's quite sure where the price is just now," Moyes said.
"We've had offers for players which we think are quite small. I can see where other clubs might be thinking there's not enough value for their players as well.
"I definitely [have sympathy for Martinez]. But I also know if I had been Everton manager and Sir Alex [Ferguson] had come asking for Baines and Fellaini, I'd have found it very difficult to keep them.
"I always thought the right thing to do was the right thing for players. Roberto is new in his job and I'm sure he'll get to understand how Everton work.
"Of course, taking their players is going to affect them, but there is not any disrespect whatsoever because we didn't make the offer public."
Moyes will manage his first competitive home game as United manager tomorrow when Jose Mourinho's Chelsea visit Old Trafford in the Premier League.
United striker Wayne Rooney has reportedly become unsettled after Chelsea had two bids for him rejected, but Moyes says he could hand Rooney, 27, a start after he came on and created two goals in last weekend's 4-1 win at Swansea City.
"Wayne has recovered and has a good chance of starting," Moyes said.
* Agence France-Presse
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