Liam Feeney gave the home side an early lead with a goal Clough felt should have been chalked off for offside, and after equalising they eventually went down to a second-half goal from Andy Keogh.
"We're not privy to the conversation between the officials and we asked the players not to approach them," Clough said of Feeney's 14th minute opener.
"The assistant flagged for offside, kept his flag up and was insistent. The referee went over and gave the goal. Why he did that I don't know. Keogh [the player offside] went for the ball and that affects everyone around him.
"We thought we should have had a penalty at the end and one at the end of the first half.
"We can't control that. We can only control our own performance and we thought we deserved to go in level at half-time."