Ton looked sluggish and slow from the outset at the weekend, a million miles from their usual energetic and confident selves.
And the Morton manager believes the visitors were well worth the win against his men.
He said: “I think there’s games that you play where you can be unfortunate to lose, but I don’t think this was one of them.
“Dunfermline deserved to win and we weren’t as sharp in any department as we would’ve liked to be.
“We had a lot of possession and pressure in terms of set-pieces but the clear-cut chances fell to Dunfermline.
“Other than Gats [Derek Gaston] making two or three fantastic saves, they could have capitalised on it. For us, we’re disappointed not just in the result but in the performance.
“We were nowhere near the levels that we’ve attained this year and we’re just disappointed that it happened.
“We’ve got to balance our season over the course of the whole season.
“And our form over the course of the season. Over the whole campaign we’ve done very well but this league is an unforgiving league.
“If you’re off the pace at all and the opposition are up for it, which they were, there’s every possibility that you could lose.
“Credit to Dunfermline, they deserved to win.”
Dunfermline were unlucky not to net a second on 73 minutes after Callum Morris was deemed to have jumped unfairly with Thomas O’Ware and referee Mat Northcroft whistled for a foul.
But Duffy didn’t see anything wrong with the goal, admitting his side got away with one.
He said: “They got a goal chalked off and me personally, I thought it was a bit harsh.
“But there were one or two decisions that we looked at as well, he’s booked Ross [Forbes] for diving and I’m not sure about that one.
“If the referee has one or two wrong, fine.
“I won’t complain too much about that, we didn’t play as well as we can play and Dunfermline were more of a goal threat.
“It’s a day where you’ve got to be honest enough to give credit to the opposition.”