The Stags lost by a solitary penalty against York City in midweek and at Sixfields Oliver Palmer gave Cox's side the lead at the interval but Darren Carter equalised with a second-half penalty after Darryl Westlake's handball, which resulted in his dismissal.
Cox said: "Once again I'm left talking about the referee and a decision that has cost my players all three points. That's two games now in which big decisions have gone against us.
"I suppose it's a good point in the end because we were down to 10 men. It was always going to be a tight game but at 1-0 up I couldn't see them getting back in it so I'm very annoyed.
"I couldn't see Northampton scoring until he gave them the penalty and to send Darryl Westlake off as well was extremely harsh.
"I thought the penalty was a nothing incident, several players went for the cross and it happens all the time. So to give a penalty for that is very frustrating and I just wish referees would give themselves a few seconds before making a big decision like that.
"Some of his decisions were very strange and some of those can have a major influence on the outcome of our season.
"I'm so annoyed, the players worked very hard against an experienced Northampton team and Alan Marriott made a couple of great saves in the second half after the equaliser. But even with 10 men we still had chances to win it and I thought Anthony Howell should have hit the target late on."