The Magpies fought back from a goal down to take the points as Conor Coady's opener for the Blades after two minutes was cancelled out by goals from Enoch Showunmi and Mark Fotheringham.
But Clough, whose side knocked Aston Villa out of the FA Cup last weekend, was left scratching his head at referee Kevin Wright's performance after he failed to give the visitors a penalty for an apparent handball by Showunmi in the first half.
"Nothing pleases me much because we certainly didn't get the run of the decisions," said Clough.
"There was a blatant hand-ball in the first half when the lad has come and blocked Conor's shot.
"We saw it from where we were, but the officials who are looking at it from 15 yards away didn't.
"We are not getting those decisions at the moment for some reason.
"I don't think it was a fair result at all. When you look at the chances we have created and the situations we have got ourselves into, we didn't make the most of them.
"They have put two good crosses into the box and scored two goals, that was it."
Liverpool loanee Coady had taken less than two minutes to break the deadlock for Clough's side, rifling home from the edge of the box following a neat one-two with Chris Porter and he almost doubled the lead three minutes later but side-footed wide.
County found their feet though and were level after 26 minutes. The dangerous Jamal Campbell-Ryce fizzed a cross into the box which hit Showunmi on the chest and bounced in.
Showunmi was almost the villain soon after, but Sheffield United appeals for hand-ball by the striker in the County box fell on deaf ears.