Hernandez snatched the decisive goal 10 minutes from time to give United a dramatic 3-2 win, but Hughes was angry that the Mexican was only shown a yellow card for a late challenge on Robert Huth just moments after coming off the bench in the second half.
The Stoke boss said: "In my opinion he shouldn't have been on the pitch anyway for the challenge on Robert Huth.
"It was a reckless challenge, I'm sure the lad would agree himself. It's dangerous and you've seen players sent off for lesser chances than that many times before. So we're disappointed with that decision.
"Why the assistant referee didn't see fit to do something about it I don't know. We were disappointed with the decision by the referee. It is very difficult to go against a 70,000 crowd here. Sometimes you have to be strong as a referee."
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