Should he be proved guilty of the charges then Wright-Phillips could face a three game suspension.
"We are disappointed," said Hughes.
"There are a few letters and faxes going to be exchanged between ourselves and the FA because the way it stands, if we decide to appeal, we are not going to get a verdict until late on Friday.
"The process could have been done a lot more quickly, which is something we will be highlighting, because I have to prepare a team for Saturday.
"By the letter of the law Shaun retaliated, but he had twice been kicked from behind. I don't think what Shaun did in response was violent conduct.
"It was a human reaction and I feel a three-game ban would be unfair."