McPhail was sent off and Colchester awarded a penalty in injury time. They scored to make it 3 - 1.
If the appeal fails McPhail will miss one game as the red card was not for violent conduct.
"I'll try and appeal against it, but I don't normally get any joy from our appeals," Jones said.
"Hopefully I'll get the referee to look at it and he'll decide it's not a red.
"They were bumping and barging each other and, if anything, Stevie says the lad was holding him rather than the other way around."