Jones drew the ire of the home fans with half an hour played when, having booked Yaya Toure just two minutes previously, he failed to produce a red after the former Ivory Coast international fouled Jordon Mutch.
Toure then went on to play a key role in City's win, scoring their third with a fine free-kick late in the second half, leaving Allardyce frustrated with the officiating.
Speaking in his post-match media conference, Allardyce said: "They should have been down to 10 men, yes, no doubt about it. Mutch had been booked for less, much less.
"Obviously that was a sending off so the referee hasn't done his job. He hasn't been consistent."
On the defeat itself, Allardyce speculated that losing and being knocked out of the cup could prove to be a blessing in disguise.
"Only time will tell whether that defeat is a blessing or not," he added. "Every game you play you want to win it. We've lost that habit of winning.
"Our game is okay in parts, we sometimes look quite good and then a mistake creeps in and the opposition punish us."