The Premier League champions this week offered a reported 28 million pounds ($43.7 million) for the pair, a bid Everton immediately dismissed as "derisory and insulting".
Moyes said that although he understood why manager Roberto Martinez, the man who replaced him at Goodison Park, wanted to keep his best players, he would have allowed Belgium international Fellaini and England's Baines to leave if he was still in charge.
"I definitely do (understand) but I also know that if I'd been Everton manager and Sir Alex had come asking for Leighton Baines and Marouane Fellaini, I'd have found it very difficult to keep them because I always felt the right thing to do was what was right for the players," he told reporters.
United are yet to land a big-name signing during the transfer window, with the deal to recruit Wilfried Zaha from Crystal Palace having been completed in January.
Martinez said United's bid lacked "common sense", but Moyes does not think it was disrespectful.
"The transfer window is open and we can make bids and you can say 'Yes or no', it's as simple as that. You are allowed to bid," Moyes said.
"That's not our choice (to make it public). That's up to them. You need to ask them that question.
"There's sort of a mixed market at the moment. No one is quite sure where the price is right. It's a sort of strange market," Moyes added.
"We've had offers for players at this club, which we feel are quite small. I can see it where other clubs might be thinking it's not enough value for their players as well."
Moyes also said unsettled United forward Wayne Rooney could start Monday's game against Chelsea, despite the London club's interest in signing him.
United have turned down two bids for the 27-year-old and Chelsea manager Jose Mourinho has not ruled out making a third.
Rooney, who wants to leave, played a limited role in pre-season but came on as a substitute in the 4-1 win over Swansea City last weekend.
"He has got a good chance of playing against Chelsea, a good chance of starting," Moyes said.
($1 = 0.6413 British pounds)