The Iron's U18 side lost 3-1 at Notts County on Saturday morning.George Barmby put United in front after 26 minutes when he ran beyond the home defence to fire home.
Scunthorpe had a strong penalty claim turned down in a good spell of pressure during the first half.
County equalised on 55 minutes from a corner and took the lead on 58 with a shot from distance.
In the last minute, United conceded from a free kick.
Academy manager Tony Daws said: "It's a big learning curve for ourselves today. As a team we gave away too many free-kicks and corners, and conceded two goals from set plays in the second half which lost us the game."
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