Wayne Rooney's tap-in seven minutes after the break was enough to seal all three points for Manchester United as Stoke suffered a third loss in their last four games.
"We didn't give ourselves any sort of opportunity to win the game, to be perfectly honest," Hughes told the club's website (www.stokecityfc.com).
"We had a poor start, allowed them to get decent balls into our box and were passive for a number of occasions on the edge of the box too.
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"We then have to chase the game in the second half and that means there's always a danger of conceding more. We kept going in the second half and tried to make things happen but it was always going to be difficult."
The loss of defender Philipp Wollscheid through injury made it a particularly damaging night for Stoke, who are struggling for defensive options with Ryan Shawcross, Marc Wilson and Geoff Cameron all unavailable.
"Philipp pulled his calf in the warm-up and was struggling from the start. It got worse as the game progressed and in the end we were forced to take him off," Hughes added.
"We'll have to check on him and I just hope we have some good news when we get back to the training ground. It shouldn't be too serious, I wouldn't think, but right now he's a doubt for the weekend."
Stoke, who are ninth in the table, host 12th-placed Everton in the league on Saturday.
(Reporting by Shravanth Vijayakumar in Bengaluru; Editing by John O'Brien)
