Playing with ten men for the last 20 minutes of play, the Iron were pegged back and eventually beaten 3-1.
Danny Elliott gave 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 allocated substitutions had been made, while Michael Kelly also suffered injury meaning Scunthorpe effectively had nine men out there at the end.
Talking through the game, Dean said: "I thought we started really well. They matched us up and went four at the back. We had a lot of really good possession and a lot of good chances. They were forced into a change, reverting to a back five in the last 20 minutes of the first half, and they had a lot of space between the lines.
"Due to that, we changed it up at half-time and went a little bit tighter, looking to play on the break a little bit in the spaces, and we looked good value and comfortable. We made a final substitution and then Dion Sembie-Ferris was injured by a late challenge. After that, Michael Kelly got a knock. We'd made our last substitution as Max Kouogun was struggling and that was a forced change.
"Dion looks like he's going to be out for a while and we had to take Michael away from the full-back area (following his injury), where he'd done really well and that's where the equaliser came from. We effectively finished with nine men really.
"I've got to say I'm pretty proud of the endeavour the boys showed. I wish we'd shown a little bit more discipline when down to nine and ten men and chasing lost causes which we didn't need to, but we also had a couple of good chances in that stage as well (including Jack Jenkins hitting the woodwork in the fourth minute of stoppage time before Brackley's two late goals).
"The game turned on the two injuries (to Sembie-Ferris and Kelly) really."
Dean added: "The medical team said Dion's doesn't look good, while we'll have to wait for Michael's to settle down and assess on Thursday. Max got a knock and we'll assess that too."