Jamie Ward scored a consolation from the spot for the Rams after home goals from Matej Vydra and Joel Ekstrand.
"We're quite pleased with the performance generally and it's little things in games, either a bit of quality - with the finish in the first half and we had a situation better than that with Michael Jacobs and he failed to get a shot off," Clough said.
"We had numerous situations and it's been a failing of ours, we don't make the most of them in the final third. Whether it's decision making or a lack of quality and then our old Achilles heel, failing to defend a corner as well has ultimately cost us the game.
"There was nothing in the game generally between the two teams. They were two passing sides, I didn't think there was a great deal, just that little bit of quality and us failing to defend the set play. Very simple things win or lose football matches most of the times, basics."
The manager could not speak highly enough of side's work-rate and added: "They're absolutely knackered again, they give it absolutely everything. I just said to them you've got to learn that you're wasting your own work in some ways.
"You're putting so much in and there's just little things that are stopping us getting a point or three.
"The second we rectify those or do whatever we can, then they'll be getting the rewards for their hard work. You can't fault their effort at all."