Deeney was sent off inside the opening 13 minutes of the FA Cup finalists' 1-0 defeat to the Gunners at Vicarage Road, after a collision with Lucas Torreira.
Speaking post-match, Gracia said of his skipper's dismissal: "I don't agree but I respect the referee's decision. It's maybe a yellow card.
“He [Deeney] doesn't have to explain to me anything. I could see the play. I could see the contact with his arm but never his elbow. I don't understand that decision.
“I never saw an aggression in the movement. I don't understand why the referee took that decision."