The Blues’ run of four successive victories was ended when Ronaldo’s devastating set-piece was followed by a cracker just before half time from Carlos Tevez, again the subject of weekend reports linking him to City.
But boss Hughes, who has now set a target of six points from the last two games to have a chance of Europe next season, was upset that Stevie Ireland was penalised for his 17th-minute tackle on Dimitar Berbatov.
He said: “At the time we were in the ascendancy and it was against the run of play. I was disappointed with the award because I didn’t think it was a foul. Stevie Ireland got the ball in a tangle of legs and the guy’s gone over.
“The kick took a little deflection off Nigel de Jong on the edge of the wall that took it past Shay. At 1-0 down there was still something in the game for us but we got caught out by a long ball. It was good control by the lad Berbatov and he set up Tevez for an outstanding strike for the second one.
“The free kick was one of the decisions that we feel a little aggrieved about. But it happens and you have to focus your mind and concentrate. The award was harsh, but give him credit, it was still a good strike.”
City’s manager will not give up the chase for the Europa League though Fulham are clear favourites after beating Aston Villa. He said: “Fulham had a good result yesterday but I don’t think anybody outside our dressing-room or fans gave us a chance of getting something here.
“The focus shifts to Tottenham, which was always a key game. The challenge is to get three points at Tottenham then win at home to Bolton in our last game. If we get six points we’ll go close. Let’s see what happens.”
City never threatened to repeat last season’s famous derby victory. Hughes added: “We felt hard done by at half time because that wasn’t a fair reflection of the game. In the second half United got people behind the ball and they are adept at the counter-attack, so you still have to keep players back.
“But we didn’t ask enough questions of them today. We just didn’t have that presence to enable us to retain possession in that vital final third and as a consequence couldn’t get enough players forward.
“In the end we didn’t have quite enough in key areas to ask enough questions of a good United side. But we gave a better account of ourselves than we did in the home game. We tried to get the ball down and play our football.
“Our shape was good. Our back four played well, and the two guys in front were good in possession. What we haven’t got is the option to go 4-4-2 on a regular basis away from home. I’m still of a view that we need a more physical presence than we have at the moment.”
Hughes will wait 24 hours to assess Robinho after the below-par Brazilian came off near the end with a groin injury. “He could be a doubt for the weekend,” admitted the boss.