Scunthorpe boss Brian Laws felt his side didn't deserve to lose after Crewe sub Ajay Leitch-Smith bagged the winning goal.
Leitch-Smith stepped off the bench in the 71st minute to grab all three points for the Alex four minutes later and end the Iron's four-game unbeaten run.
United had looked the more likely to score before goalkeeper Sam Slocombe tipped Luke Murphy's penalty on to the upright and Leitch-Smith buried the rebound four minutes after coming on.
Laws said: "The defeat is hard to take because we didn't deserve it.
"We were best team, and that isn't a biased remark, the evidence is there. We created enough chances, but we just didn't finish them off.
"The referee had let so many things go throughout the game so it is difficult to understand why he decided to give such a soft penalty.
"Tom leaned in slightly and if you look on the DVD not one of their players appealed and that gives you an indication that they didn't think it was a penalty.
"I keep stressing to the players that it is not all doom and gloom, if they keep playing like that then we will keep picking up points.
"We have a batch of home games coming up now thick and fast and we need to win those to keep ourselves in this division."