The midfielder said a key difference between the sides was that Liverpool are fighting for a Premier League title while Manchester United are "fighting for nothing".
Manchester United are long-shots at qualifying for a Champions League place with five matches to go and Arsenal and Tottenham in superior positions with games in hand.
"I apologise to the fans. It will never be enough but it's all we can do," Fernandes told Sky Sports. "They deserve much more from us. "I think everyone gave 100% and put the effort in, but we did not play well enough. "Liverpool are fighting for the title, that's the difference. We're fighting for nothing. We have to look inside and try to understand what is going wrong."