Referee Paul Taylor showed a straight red card to the Irishman for his challenge on Jem Karacan.
"It looks harsh," said Jones. "I can understand his foot is up but so is the other guy's but there's no contact."
Jones has asked Taylor to reconsider the decision and the Hertfordshire official has agreed to the request once the appeal is officially made to the Welsh FA.
Cardiff have claimed wrongful dismissal and are preparing a DVD of the McPhail incident for the Welsh FA disciplinary panel to review.
The Welsh FA disciplinary panel are set to meet to discuss McPhail's dismissal on Friday at 1400 BST.
"It's one of those challenges," said Jones.
"The ball's up in the air, he knows the player's going to hook it on. It was a yellow card at best.
"I've asked Paul Taylor to have a look at it again, but we have to appeal before he can do that."