Minutes into the second half with the game goalless, new Rovers defender Andre Ooijer clearly pulled Chelsea skipper John Terry to the turf and referee Mark Clattenburg had no hesitation in awarding a spot kick which Frank Lampard duly converted.
Moments later however, Rovers striker Jason Roberts was clearly tugged in the box by Carvalho yet no penalty was given and Chelsea doubled their lead later on through Didier Drogba.
"We all feel like we've been mugged," Hughes said after the game.
Penalty Decisions Upset Hughes
"Certainly by the decision for the penalty, John Terry has thrown himself to the ground and the referee has unfortunately thought it was a penalty.
"We've had a similar shirt-pulling incident at the other end and he doesn't give that. The decisions have to be right for both sides and they weren't.
"From our point of view the penalty totally changed the game.
"As soon as it was given it was always going to be difficult, their second goal was immaterial as we were pushing for an equaliser."