Both clubs had agreed a transfer, that would see De Gea move back to Spain, while Navas joins United, but the final paperwork was submitted in the last minutes of the transfer window.
According to reports, the deal fell through as the documents were pa$$word protected.
United and Madrid are insisting that they sent in the documents before the deadline and claim they have a time-stamp from FIFA as proof.
De Gea is yet to feature for the Old Trafford outfit this season, as his future remains up in the air, while Navas reluctantly agreed to move the other way on Monday.
A quick resolution to the matter may be reached on Tuesday, but the possibility of both clubs trying to sort out the transfer in other ways like going to the Court of Arbitration, exists.