Peter Crouch cancelled out Sergio Aguero's opener for the visitors to ensure Hughes' men went in deservedly level at the break.
But Manchester City, who came into the match on the back of a four-match winless run in the Premier League that has damaged their title defence, turned in a dominant second-half display as James Milner and Samir Nasri netted either side of an Aguero penalty.
But Milner's involvement in a seventh minute incident caught Hughes' eye - if not those of the match officials.
Crouch headed goalwards from a left-wing corner and television replays showed that Milner blocked the effort with his arm.
"I thought [in the] first half we played very well and arguably should have been in the ascendency," former Manchester City boss Hughes told a post-match press conference.
"We caused City, who are obviously a very good team, a lot of problems during the first half I felt.
"We had a clear penalty not given by the officials which are key moments in games against the top teams that you need to go for you. We didn't get that decision which seems to be a concurrent theme at the moment.
"Second half, credit to City, they came out a little bit sharper and put us under pressure higher up the field.
"We're disappointed in terms of how we allowed them the second goal - we didn't really lock them in in that area of the field and they produced the cross for the goal.
"At that point we started to chase the game somewhat and that really plays into a team with the quality of City's hands. We were picked off a couple of times and there were individual errors as well and collective errors - you can't afford to do that.
"First half I was happy with what we produced; second half we weren't quite good enough to stop City from taking the game from us."
