Phil Parkinson insisted City had been thrown out of the FA Cup because of a “very minor administrative error”.
The Bantams fielded on-loan Newcastle defender Curtis Good against Brentford with permission from his parent club but without the correct paperwork having been completed.
Good did not feature on Saturday as Parkinson only wanted one defender (Tom Naylor) on the bench but City will have their appeal against the expulsion heard in London tomorrow.
Parkinson said: “I want our supporters to know it was a very minor administrative error. The main reason I brought in Curtis and Blair (Turgott) was because I wanted to play them in the cups.
“The first question I asked Alan Pardew was ‘I’d like Curtis, but can he play in the FA Cup?’
“He said ‘yes, no problem’. It was just a line that wasn’t on the agreement and with everything going on at the club the administrative staff haven’t picked that up.”
Parkinson appeared resigned to losing the appeal as he said: “If we had drawn Manchester United away in the third round I think it would have been a massive deal and worth a hell of a lot of money.
“But in reality we’re doing really well in the Capital One Cup and the Johnstone’s Paint Trophy.
“That Brentford replay falls in between Southend away and Wycombe away.
“If we win the appeal then bring it on, but if we don’t then we’ll take it on the chin.
“I think our supporters understand that despite the cups, and we're doing well in them anyway, the league is our priority.”
Good is eligible to play against Arsenal and could earn a place on the bench as Naylor is unavailable to play on Tuesday.
Parkinson added: “Curtis has been outstanding since he’s been with us.
“He was disappointed to hear the news yesterday but it’s absolutely nothing to do with him at all.
“He’s been a credit to Alan Pardew and Newcastle. He’s going to be a very good player and we’ll enjoy working with him for the rest of his time here.”