Harry Lewis and Harrison Poulter came close in the first half, but the turning point of the game came on 52 minutes when Tyrell Sellars-Fleming scored a goal which was disallowed for offside, but after seeing a replay since the Iron coaching team are convinced it should have stood.
The hosts quickly took a free-kick, broke and scored moments later.
From then, United were trying to chase the game and took a few risks, bringing players forward.
"They were two evenly matched teams but things didn't quite go our way today," Professional Development Phase Coach Rob Watson said.
"Overall, I was pleased with the performance but disappointed with the result. Sometimes you can concede goals when trying to get things back on an even par."
United return to action with a home match against Hartlepool United at Appleby-Frodingham on Thursday (11am kick-off).
IRON: Murtagh, Cunningham, Abraham, Pike, Burden-Whittleton, Lewis (Dickinson, 70), Elliott-Bell, Robertson (Rowe, 85), Strouther (Harman, 70), Sellars-Fleming, Poulter.
