Christian Ribeiro was adjudged to have nudged Robin Shroot in the back, when he was the last man. However, the referee only deemed it worthy of a yellow card.
United suffered another defeat on the road as they lost out at the Lamex Stadium after Greg Tansey‘s free kick on 75 minutes.
The Boro midfielder curled an effort into Sam Slocombe’s top right hand corner of the goal but despite the Iron goalkeeper getting a hand to the ball he was unable to prevent the goal.
In a quiet first half it was Scunthorpe that had the better of the opening moments as they put the home side under pressure from the kick off.
Leon Clarke came close inside the first two minutes to giving the Iron the lead after Mark Duffy’s left footed cross, but he could connect and the ball drifted out for a goal kick.
Duffy then had an opportunity to score for the away side but his shot was blocked by Greg Tansley and Mike Grella’s follow up was deemed to be offside by the official.
The home side’s best opportunity, of the first half, came on 21 minutes when Lucas Akins looked to capitalise on a loose ball from former Stevenage midfielder Josh Walker, but his shot rattled Sam Slocombe’s crossbar.
10 minutes before the break, the home side were awarded a free kick on the touchline after Christian Ribeiro fouled Filipe Morais. The resulting free kick was deflected off the wall, wrong footing goalkeeper Slocombe, but captain David Mirfin was on hand to clear the ball off the line to ensure both sides went in at half time goalless.
In the second half the home side dominated proceedings first Risser saw his left footed drive saved by Slocombe, before Darius Charles climbed above Mirfin before heading wide.
The Iron’s best opportunity of the second half came courtesy of Duffy, whose late drive was parried away by Steve Arnold in the Stevenage goal.
After the goal, Tansey had a number of free kicks which threatened the Iron defence, however the home side were unable to double their lead.
Duffy and Ribeiro combined down the right wing - just after the hour mark - but the resulting cross was too deep for Clarke, who was unable to connect with the ball.
Two minutes later Clarke found the ball at his feet, his shot - from the edge of the area - stung the gloves of Arnold, but he reacted quick enough to prevent the corner.
In added time Stevenage, once again, came close to doubling their lead. Niall Canavan and Gibbons got caught up on the half way line, before former Arsenal youth prospect Luke Freeman raced towards Slocombe’s goal. He attempted to chip the Iron goalkeeper from the edge of the area but he could only find the advertising hoardings in the stand.
Arnold, Charles, Tansey, Dunne, Haber, Morais (Freeman, 70), Akins, Roberts, Comminges, Risser (Grant, 59), Shroot (N'Gala, 90).
Substitutes not used:
Grant, Freeman, Day, Ball, Rogers, Lopez.
Scunthorpe United:Slocombe, Ribeiro, Mirfin, Canavan, Newey, Walker, Ryan (Sedgwick, 73), Duffy, Gibbons, Grella, Clarke
Substitutes not used:Severn, Kennedy, Reid, Barcham, Jennings, Keegan.
2,953 (200 away approx).