Duffy's first-half strike was levelled by Nick Powell, as the Iron gave a runout to David Mirfin - captaining the side - for the first time since he rejoined the club, and included Irish trialists Mark Hughes and Jordan Keegan in the matchday squad.
The visitors had the ball in the back of the next after just three minutes, but Federico Macheda was well offside and no goal was given.
The Iron's first real effort came after 10 minutes through a low shot from Duffy, which clipped a visiting defender and spun away for a corner. The ball in, a first test for returning Sam Johnstone, was punched conifdently away by the youngster.
The first real chance for the visitors since opening exchanges came on the quarter-hour mark. Jesse Lingard had an effort from just outside the area, but it was straight at Sam Slocombe who held well.
Nick Powell, signed by the Red Devils from League Two side Crewe in a deal which could be worth £6million, was the next to try to beat Slocombe from range. His piledriver was well executed, but straight at an unruffled Slocombe.
The Iron took the lead after 22 minutes thanks to tenacious play from Miike Grella and Bobby Grant. Summer signing Grella won the ball near the half-way line and got away from two defenders, before feeding Grant.
The former Accrington man, who has said he wants to be more of a team player this season, kept his man at aby before slotting the ball over to Duffy, who controlled and placed a shot into the bottom right corner.
That gave the home side plenty of confidence, and their passing was as good as anything the far more expensive visiting youngsters could muster. Davide Petrucci, the visiting captain, reminded Slocombe he was still there with a snapshot that - again - was straight at the home keeper.
A moment leater, Bebe - playing on the right wing - flashed a low shot just wide of Slocombe's far post and Powell headed well over from a Bebe cross, really should have been closer to the target.
Grant stung the palms of of Johnstone after 38 miutes with a shot, possibly intended as a cross, and there was a tame appeal five minutes before the break when Robbie Gibbons went down in the area under pressure from Michael Keane. The referee was not interested, meaning the score remained 1-0 at the interval.
Fans in the home terrace gave Johnstone a round of applause as he returned to spend the second 45 minutes in front of them, while there was also a moment of appreciation for physio Alex Dalton as he was present at his last game in the role after seven years of service.
Slocombe had to be awake to turn away a shot from Powell three minutes after the restart, though he needed both hands to palm it away.
A second penalty claim from the Iron was waved away when Grella went past several defenders to get to the byline and went down after an apparent shove from Keane. Again, the referee was not interested.
The sides were level after 51 minutes, however, when Lingard played the ball across the area to an unmarked Powell who fired past Slocombe.
Macheda sould have given the visitors the lead shortly afterwards, with Lingard again the provider, but his attempt to beat Slocombe at the near post went wide.
Iron fans got their first chance to see trialist Hughes with 20 minutes to go, as he came on in place of Gibbons.
Connor Jennings also got a runout with 15 minutes to go, replacing the impressive Grella, with Hughes.
Both sides had late chances to win the game, with Petrucci firing over for the visitors and Jennings flashing an effort wide for the Iron before smashing the last shot of the game straight at Johnstone.
Scunthorpe: Sam Slocombe, Christian Ribeiro, Josh Walker, David Mirfin (c), Bobby Grant, Mike Grella (Jennings), Andy Barcham (Keegan), Robbie Gibbons (Hughes), Niall Canavan, Mark Duffy (Godden), Tom Newey.
Subs: James Severn, Connor Jennings, Matt Godden, Callum Howe, Eugen Bopp, Connoy Smythe, Charles Vernam, Mark Hughes, Jordan Keegan.
Manchester United: Sam Johnstone, Marnick Vermuil (Cole), Robbie Brady, Ryan Tunnicliffe, Michael Keane, Scott Wootton, Bebe, Nick Powell, Federico Macheda, Davide Petrucci (c) (King), Jesse Lingard
Subs: Larnel Cole, John Sutherland, Joshua King, Luke Givern, Freddie Veseli, Tyler Blackett