The Iron were defeated 2-1 in their latest Youth Alliance League game, as Grimsby Town kept up their unbeaten run in the competition.
Patrick Virgo netted Scunthorpe's goal on the day, with Joey Dawson seeing his goal - which would have put the side 2-1 up - controversially ruled out for offside when replays suggest the forward was onside when the ball was played to him on the edge of the area.
The Iron were looking to avenge for the FA Youth Cup defeat at Blundell Park earlier in the season and were on course to do exactly that when they took the lead. However, the hosts got two goals, including a late strike, despite United's dominance to take all three points.
Professional Phase Development Coach Steve Thornber said: "It was a good performance against a strong Grimsby Town side who beat us in the FA Youth Cup. We dominated large periods of the game, had some really good passing movements and had a number of chances.
"Overall, it was probably one of our best performances of the season. We played some really good football and we'd had chance to work on a few things with the lads that have come back in."
Scunthorpe took the lead on 18 minutes when the ball was worked out wide to Harry Baker. His cross found Virgo, who sent his header into the net.
Shortly after, Virgo could have double his and the Iron's tally, but his latest effort went wide.
Just two minutes after the Iron's goal, the Mariners were level. The hosts counter-attacked with a cross coming into the area, which was headed home.
On 25 minutes, Under-15s player Harvey Cribb sent a 25-yard effort wide of the target.
Five minutes later, Joey Dawson was to have the first of four opportunities in the game. He was played in by Cam Wilson, but Dawson's effort was blocked by the goalkeeper.
The Mariners' efforts were all on the counter attack, with Jake Balme making a fine save to push out an effort which was destined for the bottom corner.
Oliver Kemp rose highest from a corner soon after, but his effort went just over the bar. Meanwhile, just before half-time, Dan Gallimore broke forward, but didn't get the rub of the green as he couldn't angle an attempt on target.
Ten minutes into the second-half came the game's big talking point. A free-kick was awarded to the Iron and taken quickly into the feet of Dawson, who fired a shot across goal and low into the corner of the net, but the effort was ruled out controversially for offside and the score remained 1-1.
Dawson had his latest opportunity soon after as he latched onto an Oliver Lobley cross, but his side-footed volley went just over the bar.
On 71 minutes, Dawson would be frustrated again after he worked hard to turn and find an opening inside the penalty area, only to see his effort go wide of the target.
Soon after, Virgo was the latest to fire over after good team build-up and a succession of passes inside the Grimsby half.
On 84 minutes, Grimsby netted what proved to be the winner as a loose ball dropped inside the Iron's penalty area, with the Mariners player reacting quickest to send the ball agonisingly into the corner of the net.
Two minutes later, the Iron had their final chance to restore parity through Virgo, but his header went just wide of the target as he connected to a Jamie Moore cross.
The side are next in action away at Rotherham United on Saturday, December 5th (11am kick-off).
IRON: Balme, Baker, Dawson, Gallimore, Kemp, Elliott-Bell, Lobley (Moore, 70), Virgo, Wilson, Young, Cribb.
IRON UNUSED SUBS: Foster, Griffin, Strouther.