Just seconds after replacing Tom Cleverley, the Mexican caught Robert Huth with a high tackle that incensed the Stoke players and coaching staff.
Referee Lee Mason booked the striker before he headed in Patrice Evra's cross to seal the points, and former United man Hughes was disappointed the referee had not given the forward his marching orders.
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"It was a poor challenge on Robert Huth, and reckless in my view. Why the assistant referee didn’t see fit to do something about it I don’t know.
"It was a reckless challenge. You can’t raise your leg like that and you’ve seen it many times before where players have been sent off for lesser offences."
Hughes, who remains stuck on 99 Premier League victories as a manager, also believed that the vocal home crowd may have influenced Mason.
"I think referees and assistants see what they see and make decisions accordingly. There was a 70,000 crowd here, and they have a big influence on people, not just referees.
"At times you have to be strong as a referee as well."
Manchester United manager David Moyes, meanwhile, was thrilled with his side's comeback, though he admits they were still not at their best, especially in the first half.
"I thought we did a lot of good things but an awful lot of really poor things which put us in the situation we were in," he said.
"I thought some of the play we had was very good but it wasn’t leading to any goals. We went in at half-time on a downer but I said to the players that the job’s to go and win the game and they are more than capable of doing it.
"I thought we were very worthy of getting a goal back. We knocked on the door and couldn’t find ways through.
"At times I thought our play was good but we couldn’t find the final touch again."