Playing with ten men for the last 20 minutes of play, the Iron were pegged back and eventually beaten 3-1 at Brackley Town in their FA Cup second qualifying round replay on Tuesday night.
Danny Elliott gave Jimmy Dean's side a first half lead but an 86th minute equaliser, followed by two goals deep into stoppage time, ensured the hosts got through to the next round.
United were a man down for the final stages of the game, as Dion Sembie-Ferris was forced off through injury after all the alloted substitutions had been made.
There was one change from the side that lined up for Scunthorpe on Saturday, as Richie Bennett came in for Danny Whitehall up front.
On six minutes, Michael Kelly did well to track the run of Cosmos Matwasa before sticking a boot in and taking the double ricochet to win the Iron a goal kick.
Just a minute later, Cameron Wilson was away down the right flank and hauled down by Riccardo Calder. There was no card for the left-back, but a stern word from the referee.
Then, Maxim Kouogun made the run from Jacob Butterfield’s right-footed delivery, but the hosts turned the ball behind for a corner.
Soon after, Will Evans almost seized on the loose ball from a Butterfield, but the ball skipped up for Bennett, who sent his half-volley wide of the target.
There was then patient build-up from the Iron which involved Wilson and Shrimpton, which culminated in Butterfield dinking into the area to meet the run of Tyler Denton, who was flagged offside.
On 15 minutes, there was good work again from the Iron before Bennett held up play and fed Shrimpton. Butterfield then got the ball, sidestepping one player before his long range effort took a deflection, which Danny Lewis got down to save.
It wasn't long until the Iron dugout was incensed as Bennett held the ball up and turned it round the corner for Denton. He was clearly hauled down by George Carline in front of their eyes, but nothing was given.
The hosts came close in the 24th minute when Dan Turner cut in from the left and unleashed a right-footed effort which looked destined for the bottom corner, but for the leg of Kouogun, resulting in a corner to Brackley.
Just a minute later, United took the lead as Bennett picked the ball up, turned to his right and saw Elliott in space. He fed him through on the left, with Elliott advancing on goal before slotting across goal into the corner for his fourth goal of the season.
On 28 minutes, Ross Fitzsimons was drawn into a superb save as he pushed away a goal bound header from merely a couple of yards out as the hosts looked for an immediate reply.
In the 32nd minute there was an opening for the Iron as a quick move opened up space for Wilson to be slotted through. The pass was slightly heavy, allowing Lewis to gather despite the best efforts of the Iron's No 11.
Shortly after, a superb first touch from Bennett opened out the space. He slotted the ball down the left with a low cross into the area seeing Kelly and Lewis challenging, with the Brackley ‘keeper coming out with possession.
On 35 minutes, Newton got into space in the box after opening up onto his left foot, but the low effort was straight at Fitzsimons, as he gathered comfortably.
Four minutes later, home substitute Turner was again denied by Fitzsimons before Evans swept up the rebound with Newton lurking.
Two minutes before the interval, Fitzsimons flew to his right to once again deny Turner an equaliser before Wilson hooked the ball clear for a throw.
In the third minute of first half stoppage time, Wilson stole possession inside the box but saw his cutback intercepted. Meanwhile, Kelly got the first yellow card of the night following a pull-back on Matwasa.
There was a Scunthorpe change at half-time, as Wilson was replaced by Dion Sembie-Ferris.
Three minutes into the second period, Brackley were awarded a penalty after a sliding challenge where it looked like the ball had been clearly played. Bennett was carded for dissent, with the Iron players fuming at the decision.
However, Fitzsimons guessed correctly, saving Danny Newton's spot-kick, and the rebound was smashed onto the top of the bar and over for a goal kick.
In the 55th minute, Elliott seized on a loose pass before cutting left and hitting an effort hard, but just over the bar.
Three minutes later, at the other end, Turner sent his latest effort from just outside the box over the bar.
Shrimpton was next to be shown a yellow card on 60 minutes when he dragged back an opponent.
The hosts pressed for a leveller as the second half went on but United stood up to what was thrown at them.
There were then two substitutions in quick succession, as Whitehall came on for Bennett and Kouogun was replaced by Andrew Boyce.
On 77 minutes, Sembie-Ferris was sent to the ground off the ball by Shepherd Murombedzi. The Iron substitute required treatment and looked in quite a bit of pain, eventually being unable to continue.
The Iron resumed the match with 10 men, with the latest Brackley attack seeing Turner send a flying header across goal and wide.
In the 85th minute, Brackley rushed with a free-kick and played it straight to Butterfield, who advanced on goal and saw his shot blocked. Handball shouts were turned down by the referee.
Then, just a minute later, Tyler Lyttle sent a side-footed volley into the corner of the net to level proceedings.
There were nine minutes of stoppage time and, in the fourth of those, there was a corner to the Iron as Evans teed up Kelly, with his goalbound shot deflected wide.
Boyce ran to the front post and connected well with Butterfield’s corner, but Lewis saved.
Brackley then broke, with another fine save from Fitzsimons down to his left as he pushed the ball around the post for a corner.
Evans turned a shot from Dominic McHale around for a corner, just before Jenkins' effort struck the crossbar in the seventh minute of stoppage time. Fitzsimons threw his body at the ball and the Iron broke with Whitehall, and the Leeds loanee struck an effort which cannoned back off the woodwork.
There was to be late success for the hosts against United's ten men though, as Newton sent an extraordinary effort into the net off the underside of the bar in the eighth minute of stoppage time.
There was then a penalty to Brackley and a yellow card for Evans as McHale broke the offside trap and went down. The player then stepped up to score.
United return to action in the National League North on Saturday with a trip to take on Chorley.
BRACKLEY: Lewis, Carline, Calder, Murombedzi, Dean (Turner, 21), Matwasa, Bates (Cross, 75), Newton, McHale, Lyttle, O'Sullivan (Armson, 83).
BRACKLEY SUBS NOT USED: Roberts, Crawford, Worby, Tibbetts.
IRON: Fitzsimons, Kelly, Kouogun (Boyce, 75), Evans, Elliott, Wilson (Sembie-Ferris, 45), Bennett (Whitehall, 73), Butterfield, Shrimpton, Jenkins, Denton.
IRON SUBS NOT USED: Chapman, Smith, Barrows.
ATTENDANCE: TBC.