The home side looked like they had earned a point from the game after they equalised in the 87th minute.
But they reckoned without big Aussie Brett Emerton who stole the points for Rovers four minutes into injury time.
Holloway felt there was a suspicion of offside and that Gary Taylor-Fletcher was fouled in the build-up to the goal. He claimed overlooking the incidents were among several questionable decisions by Dean.
He said: "I thought the referee had a poor game and he is going to report me for what I said to him in the tunnel.
"I can't believe what he saw. I thought there was some unbelievably strange decisions out there. I waited for him in the tunnel. Never mind, I have got to learn and I should know better - but it is ridiculous."
Holloway added: "In life sometimes you don't get what you deserve, but all I can do is keep monitoring the level of our performance and I was absolutely delighted with that."