The Hornets moved into the automatic promotion places thanks to goals from Matej Vydra and Joel Ekstrand although Jamie Ward's penalty ensured a nervy finish for the hosts.
But for Clough it was a familiar tale as some wayward finishing and poor defending at set pieces cost his side dearly again.
"We're quite pleased with the performance generally and it's little things in games," he 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.
"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."