The former Galabank player struck twice to end his club's 10-match winless run, but despite being pleased with the win, Duffy said he felt the player should have enjoyed his strikes.
He said: "I can never understand when I see players scoring goals and then not celebrating.
"The team that pays the money is the one you have got a duty to, not the one you left behind.
"Bryan still trains the Under-17s at Annan, but he was well within his rights to enjoy the goals.
"There were some top-class performances from my players."
Elsewhere, Queen's Park ended their recent poor run with a 2-1 win over bottom club Stirling Albion, and Montrose ran out 2-0 winners as Peterhead continued to struggle on the road.
In yesterday's fixture, Berwick Rangers edged past East Stirling 1-0.