Adam Johnson's first effort was saved by Joe Murphy, before he was felled by the Irons keeper and coolly converted at the second attempt.
Scunthorpe boss Nigel Adkins: "I think when we analyse the video and when we analyse the last time we were in the Championship and the penalty decisions that went against us that weren't penalties, is there a trait coming out there?.
"The turning point for the scoreline is the penalty, it's not a penalty. Michael O'Connor has tracked his runner, it's a fantastic tackle and the referee has made a mistake there. Joe Murphy makes the save and the second one is a penalty in my view because Joe has made a fantastic save but he's dived at the player's feet who has just got to the ball first.
"The second is a penalty, the first is not. But great credit to the players because we kept taking the game to Middlesbrough. Michael has made a decision on what he thinks is right for the penalty. As it is, it's a wrong one."