"You do discuss it before every game," said Hughes, who confirmed QPR would appeal against the decision.
"You worry more about decisions going against you and it shouldn't be like that.
"You should have confidence that the referee will get the key decisions right.
"Just lately a lot of managers have lost faith in them.
"It is a difficult job. You have to be strong and really clear.
"You have to be 100 per cent right to give the decisions. At the moment people are guessing and hoping that they get it correct. That was the case today."
Even Sir Alex Ferguson admitted Young was offside, although he did claim Derry's early exit had a negative effect on his own side.
"Ashley was a yard offside and I understand why Mark is angry," said the United chief.
"There have been a lot of decisions like that in the last few weeks.
"It didn't help us at all. I was more confident before the man was sent off because the speed of our play and the movement was very good.
"After that we were just in a comfort zone."