Jim Jefferies also admitted he was missing an entire team through injury and even Ryan O'Leary had to play with a broken nose.
A dispirited Jefferies said: "Hibs deserved to win the way they did, but it was always going to be a tough game coming here with the guys we have out.
"But the penalty was the second goal and I don't think anybody in the ground thought it was ever a penalty.
"John Collins and Tommy Craig looked at me, shook their heads and didn't think it was a penalty. The player fouled said to Frazer Wright he didn't think it was a penalty.
"But the only one that matters in the ground is Stuart Dougal and he's seen something, yet different from everyone else in the ground.
"The linesmen didn't put up his flag, so it was totally the referee's decision. But if you say too much you get into trouble.
"It came at a bad time and we feel hard done by, but when things are going against you, it didn't surprise me."