Harrison Ashby's effort in the 33rd minute gave the visitors a deserved lead at the break, but were made to pay for a poor second 45.
Andrew Hughes drew the hosts level, before Duane Holmes struck with just over ten minutes left to complete the comeback.
Defeat added to Swansea's misery after losing Joel Piroe to Leeds earlier in the week.
"We were dominant in the first half, so in the end I'm frustrated," said Duff "We knew we'd have to tweak one or two things at half-time, so we did that and then we didn't look enough of a threat early in the second half.
we "There needs to be a mentality shift should know that teams are not just going to roll over. We need to be putting teams to the sword.
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