The United goalkeeper appeared set to join the Spanish giants, as had been predicted for months, after the clubs agreed a deal believed to be worth around £29million on Monday.
But the Spanish transfer deadline was set at 11pm on Monday and for some reason all the paperwork was not processed in time.
United have insisted the fault did not lie with them and have proof they submitted their relevant documentation in time
Real could have the option to appeal to La Liga or world governing body FIFA over the matter but they may now have to wait until January at the earliest to sign the Spain international.
As the fall-out over the De Gea deal was being dissected, United were trying to focus on concluding other business before the Barclays Premier League's deadline of 6pm.
After the departures of Adnan Januzaj, Javier Hernandez and Anders Lindegaard were confirmed on Monday, negotiations were continuing to complete the £36million signing of 19-year-old Monaco striker Anthony Martial.
The France Under-21 international travelled to Manchester on Monday and, if completed, the deal would represent a world record fee for a teenager.
There were also suggestions 19-year-old striker James Wilson could leave United in a loan deal.
Some business was concluded in the morning with Everton finally announcing the signing of River Plate defender Ramiro Funes Mori for £9.5million.
The deal had been long expected but the size of the fee was surprising with initial reports having suggested it would be around the £5.5million mark.
It was unclear why the figure had risen but there were some paperwork issues which arose after Funes Mori attended Everton's clash with Manchester City nine days ago and it seemed then that confirmation was imminent.
Manager Roberto Martinez insisted Funes Mori was coming in to complement John Stones and Phil Jagielka rather than replace the former, who has been the subject of considerable interest from Chelsea.
And so it seemed like proving as Chelsea appeared to have given up hope of prising Stones away from Goodison Park in the summer window after failing with three bids, the most recent of £30million, for the England international.
Chelsea instead signed Senegal defender Papy Djilobodji from Nantes, with the Ligue 1 club confirming the transfer had been completed.
West Ham were another busy club
They began the day by confirming the return of midfielder Alex Song for a second season on loan from Barcelona and following up by capturing Chelsea winger Victor Moses, also on a season-long loan deal
The club then announced striker Nikica Jelavic had signed on a permanent deal from Hull.
There could also be more business at Upton Park with reports linking Tottenham striker Emmanuel Adebayor with a switch across London.
Source : PA
Source: PA