Shaun Williams' penalty and Dean Bowditch's free-kick handed the League One side a 2-0 win and a place in the fourth round.
But it was not the decisions that led to the goals that irked Jones, but the overall performance of match official Lee Collins.
He said: "The two goals we've given away are our errors - they are simple things to stop but we didn't do it.
"It was a penalty and we were fortunate to get away with a second one but, listen, the referee had a shocker.
"He allowed Smithy (Alan Smith) to run the game.
"At the end of the day he might as well have given the whistle to Alan because he ran the game.
"My players weren't going to tell him so someone had to tell him.
"He's booked people but all credit to Smithy because that's what a senior player will do if he's allowed to do it.
"I just thought it was too big a game for him. He lost it somewhere along the line and that can happen, so he's had a bad day at the office."