The Potters, who are without a Premier League win this season, lost the tie 2-1 at Bet365 Stadium and will now face West Bromwich Albion in the league at home on Saturday.
Stoke scored first through Marko Arnautovic in the 24th minute but conceded to Ryan Mason on the stroke of half-time before Markus Henriksen won it late for the Tigers on what was a disappointing night for the Staffordshire outfit.
Hughes said: "The key now is we have a big game at the weekend and we have to pick ourselves up.
"I thought there were good elements to our play tonight, so that is an encouragement for us.
"It was an undeserved victory for Hull, I felt. But that is what they have got, so we have to dust ourselves down and get going again."