Blues striker Didier Drogba was injured in the Fulham penalty area when Essien - who was sent off for a two-footed lunge on Clint Dempsey in injury time - headed home and Hughes conceded his side were caught off guard.
"The guy has jumped in with two feet, so it's a straight red," declared Hughes.
"As for the goal, that's a disappointment from our point of view. We were distracted by Drogba lying prone in the box. You still have to play to the whistle, so maybe we were guilty of expecting the referee to blow up.
"He didn't and we paid the penalty. It's confusing the way the game is viewed in terms of when players go down: are they faking, and do you kick the ball out?
"We had that in the second half when we had the ball in a promising position and ended up having the ball put out near our goal-line which was a bit ungentlemanly."