Ludovic Sylvestre's stoppage-time winner was the difference between the two
sides after the hosts had missed a penalty and seen Gary Taylor-Fletcher's opener equalised by Ben Davies.
Derby are safe for another year but with only four league wins on the road, it was a frustrating afternoon for the Rams and Clough was adamant his side deserved a point.
"There was nothing in the game, I thought we edged it second half and we were going to go on and win the game but we end up losing instead of getting a guaranteed point," he said.
"We thought our performance warranted at least a point today. We just vacated the edge of the box in the last few minutes, which we are disappointed with.
"Out of the three centre-halves we had in the area, one of them should have been in the area where the ball was struck. But it's a brilliant strike.
"We feared the worst with the decision that was made with the penalty because it was then continued for the next 60-odd minutes. The players are very angry at losing because we hate it, but also they are very angry and upset at the officials' performance - all three of them.
"You start to doubt a little bit with some of the decisions that were made."