Referee Lewis sent off Bradford midfielder Jon Worthington for a second bookable offence in stoppage time and also booked nine other players - four from the Bantams and five from Northampton.
Striker Jake Speight put Bradford in front from the spot after eight minutes when Cobblers right-back Seth Nana Ofori-Twumasi handled Kevin Ellison's cross.
But Shaun Harrad equalised for the visitors after 59 minutes after he had been brought down by defender Lewis Hunt.
Jackson said: "I was disappointed with the referee's performance. There were too many cards and I was also disappointed with the Northampton penalty and the sending off.
"I thought Jon Worthington slipped for the foul for which he was sent off. "e didn't play as well as we have been doing. We didn't really get going. We got the perfect start with Jake Speight's penalty, but I couldn't understand why we were a bit flat."
Source: PA
Source: PA