Callum Reilly's first senior goal looked certain to give the visitors three points until Adam Hammill struck deep in added time.
And Clark said: "I am gutted about the result. The key for us is to kill teams off. When the opposition are only one goal down then they have always got a chance.
"When you are 40 seconds away from the end and you concede an equaliser it is a kick in the guts and we have to bounce back."
Clark clung to the positives, which included Reilly's contribution and another decent performance from his side.
He said: "Callum was ill during the week, but put himself forward to play. He has scored his first goal for the club and should be immensely proud of himself.
"I am excited by how we have played in the last seven or eight games, with the exception of Bolton (where they lost 3-1). We are playing a brand of high-tempo passing football that I like to play."