Hughes also felt Pajtim Kasami should have been sent off after flinging an arm out in the direction of Erik Pieters.
After Darren Bent's 83rd-minute winner for Fulham, Hughes said: "I thought we had a lot of control of the game. We are trying to create opportunities for ourselves.
"We did that, had clear opportunities from corners and set-plays and had good opportunities to pick the right pass, but never quite did it.
"But, in terms of the team most likely to win the game, I thought it was totally us.
"I think if everybody at Fulham was honest with themselves, I think they will agree they maybe got a bit fortunate to take three points out of that game.
"We should have two penalties and the boy Kasami should have been sent off, in my view, because he raised his hands. If you do that, then the boy has to go.
"They were key moments that shape the game and the outcome of the game. They are the ones you want the referee and officials to get right.
"Unfortunately, it affected us in a negative way because, given the time of those incidents early in the first half, it would have obviously swung the game totally in our direction.
"As it was, we were still trying to force the issue when they got a break through a misplaced pass from ourselves. They were able to play the ball in the box, a couple of ricochets and it lands at Darren Bent's feet - the one guy you don't want in those situations. I think that was their one shot on target in the whole game."