Hughton deployed Kei Kamara, on loan from Kansas City, alongside Holt in attack, and started with two out-and-out wingers before Anthony Pilkington was forced off with a hamstring problem.
He said: "I decided to go 4-4-2 today, which means you can perhaps be a bit more open, but I thought we had the better chances.
"We certainly should have been given a penalty in the first half when Shaw pulls back Grant Holt, so on balances we deserved one today.
"Grant has got himself ball side of the defender, and I think there is contact, so the referee has to make that decision, and he also has a linesman on that side.
"If we think that one was soft, the one in the first half wasn't.
"It was not a particularly bad penalty, and the lad has made a good save."