Blackburn were 2-1 down at Eastlands with six minutes remaining when Roque Santa Cruz headed home his second goal of the game.
But the goal was shrouded in controversy as assistant referee Darren Cann had initially flagged for offside as David Dunn was in an offside position when David Bentley's cross came in.
Although Dunn jumped for the ball he did not make contact, so Cann felt he did not interfere with play and reversed his decision.
The former Manchester United striker criticised FIFA for creating a "grey area" in the law and has called for the world governing body to clarify the rule.
"It came down from FIFA and (president) Sepp Blatter to make the game more open and benefit strikers, but it makes the assistant referee's job a great deal harder," Hughes said.
"Maybe it was introduced with the right intentions but a lot of these directives are brought down by FIFA by people who have never played the game and don't understand how it will actually impact at the level that we play.
"I think most people would like it to be clearer just to have a concise understanding of exactly what the rule is.
"The way the offside rule was when I was plying my trade was a lot clearer, everybody understood it and it was easier to work on defensive situations.
"These days it's very difficult to do defensive work when there's an interpretation in the law about whether players are active or not.
"Sometimes you will benefit from those decisions, sometimes they will go against you."