"From my point of view, the ball was clearly over the line in the first half. The referee's got himself in the right position, but if he looks at the video I'm sure he'll see that he got it wrong," Hughes said after the 1-0 defeat at Ewood Park.
Ivan Campo went on to score for the visitors in the second half and then Rovers missed two penalties in the last five minutes.
"With the penalties, I thought probably the first one on Brett Emerton in the first half was a real strong claim and probably more conclusive than the two given late on in the game. But I certainly thought they were both definite penalties," Hughes added.
"I thought our general play in the first half was as good as we've played this year, but we needed a break when we were playing well.
"We just switched off for the corner when they scored and Bolton are probably the best in the league at holding onto a lead.
"On other days, we'll not play as well, but still win convincingly. Although we've missed three penalties this season, all of our guys that step up to take one are confident and I've seen Benni and Jason dispatch many penalties in training."