Hughes believes his side deserved to hang on for at least a point after an heroic effort to end a winless run at Old Trafford stretching back to 1976.
Hughes said: "I do think it was unjust, in terms of what we produced, the effort we put in and the chances we created.
"I certainly felt in the first half we could have been three or 4-1 to the good in terms of chances created. I didn't think United created much apart from the key moments that took the game away from us.
"We're really disappointed given the level of performance we produced. We had a game plan today which needed commitment, it needed people to be brave and do the hard yards that affected the game, and that's what we did.
"I thought my players were excellent, they took the game to United and really shook them."
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