Blackburn director of football Gregg Broughton says their failure to sign Nottingham Forest's Lewis O'Brien and fellow midfielder Ethan Brierley from Rochdale is "frustrating and annoying".
O'Brien had agreed a loan and Brierley had been due to sign permanently.
"I'm devastated, as are both players," Broughton told BBC Radio Lancashire.
"This was not a case of waking up on deadline day and saying 'let's sign Lewis O'Brien'. There had been a six to eight week process leading up to it.
"We failed to get the players registered and I carry the buck for that. All the hard work had been done and that is why it is so frustrating and annoying. Those players should be training here today.
"I can understand the fans' frustrations and I can only apologise on behalf of the football club. We had clear targets for what we wanted to do this window and we got within touching distance of doing that - I take responsibility for that."
In a statement on Thursday the Championship club said "complex" negotiations and "events beyond our control" led to the documents being submitted late for the first of the two rejected deals.
For the second, they cited "unsigned paperwork and technical issues".
They have until Tuesday to submit documents to the EFL to support their case.
Broughton said he is realistic about the club's chances of getting the initial decision to refuse the transfers overturned.
"There are internal and external reasons for why the signings didn't get over the line," he added.
"We can only control the internal bits and we have to review why they failed. I do think the external reasons are good but, in my knowledge, nobody has ever won one of these cases against the Football League.
"I think if you really believe in something then you have to try, and if you want to support the players. We're realistic about what the outcome could be."
The failed transfer has left O'Brien, 24 facing an uncertain second half of the season.
The agreement between Blackburn and Forest would have seen him join Rovers on an £8.8m permanent transfer, should the Lancashire club get promoted this season.
He has now not been named in Forest's 25-man Premier League squad, so his only options for playing between now and the end of the campaign would be a transfer to a club based in a league where the transfer window is still open, such as Austria, Turkey and Croatia.
Rochdale said in a statementexternal-link that "discussions continue between the clubs with the aim of concluding the transfer at the earliest opportunity" over the sale of 19-year-old Brierley, and Broughton said that Rovers "must ensure that income can go to them and Ethan can be a Blackburn player".
