The visitors were beaten 3-0, but the scoreline did not do justice to a game which saw Peterborough miss a penalty and Derby lose Jake Buxton to a red card with the score 1-0.
The outcome would have been different had Theo Robinson accepted a simple opportunity to equalise, and Clough said: "It was one of those games where everything that could do wrong did.
"We felt Jake was unlucky to be sent off as it looked like he won the ball before making contact with the player when picking up his second yellow card, but it is difficult to criticise a referee when your team has just lost 3-0.
"The final scoreline might be a tad harsh but you can't really have too many complaints when making the sort of errors we did for two of the Peterborough goals.
"We also had as good a chance to get back into a game as you will ever see when Theo hit the post, but we couldn't take it."
A mistake from goalkeeper Adam Legzdins gifted the home side their second goal, and Clough said: "I'm glad it wasn't a game-changing moment because, just like in recent games, he had been outstanding."