United were looking to win the FA Cup for the first time since 2004, but a goal from Leeds ace Jermaine Beckford sent the Red Devils crashing out.
“We had players out there who play for Manchester United and they did not perform as expected of them,” Phelan said.
“I don’t think we did ourselves justice against Leeds in certain departments of the field.
“This is a major blow. We need to be in finals of cup competitions like this. To go out at this stage is unacceptable.”
He added: “Normally, we either go experienced, or we go youth. This time we picked a bit of a mixture and it didn’t work for us.”