Clough was also furious with referee Carl Brook's decision to send off George Lapslie just after half-time for a high challenge.
“I thought we were very good tonight as the away side at top of the league,” said Clough.
“I've just said to the players – when you win games like we did on Saturday, everybody is bubbling. And so they should be.
“But things like what we saw tonight in the face of the adversity we had to endure make me think we are going to be all right in the last seven games after seeing that.
“We had no Rhys Oates, no Jamie Murphy and we had to make a couple of substitutions at half-time as, when players are on yellow cards and a referee not quite sure of the kind of decisions he's making – as we saw with the sending-off, we had to make them.
“Oli Hawkins is on 13 bookings now, so if he gets two more he misses three games.
“If you take all that into account I thought we were good tonight.
“They are the best team in the league, they don't concede many at home, and I thought they were very wary of us.”
On the penalty he said: “I don't think it changed the game as I still think we played pretty well, but I thought it was an incorrect decision.
“You don't work with more more genuine and honest lads than George Lapslie and you saw his reaction on the pitch and his reaction in there after the game.
“He didn't make contact with the player. And the referee is five yards away.
“There was certainly contact with the early tackle on Matty Longstaff after about 10 seconds, which I thought was the worst tackle of the game, and he didn't book the player.
“We were told there was blood from the gash when Laps hasn't touched the player. There was no blood whatsoever.
“The lad got up, played the rest of the game, committed maybe five or six fouls and avoided a yellow card himself tonight which is puzzling.
“The official certainly didn't cover himself in any glory tonight.”
Clough's men did have their chances in a tight match.
“I thought we started the game brilliantly and created a great chance that Lucas (Akins) screwed wide. That could have changed the game if it had gone in,” he said.
“We were pressing right to the end.
“I thought we had the best opportunity of the second half with Matty Longstaff. A little bit more conviction and he might have scored.
“Bish (Nathan Bishop) has had a couple of saves and he has done very well tonight with crosses and things, but we take an awful lot of heart out of tonight, though no points which is what we need at this time of the season.”