Stoke booked their place in the quarter-finals of the competition via a penalty shootout after 10-man Birmingham City fought back from 3-1 down to take the tie to extra-time, and then came from behind again to leave the score 4-4.
Shawcross described Stoke’s performance as “very disappointing” and called for a big improvement in Saturday’s home Premier League against Southampton.
Hughes has backed his captain and dismissed suggestions the comments may have harmed morale within the squad.
"Ryan was just making the point that in similar circumstances in future there would be a different mentality and a better focus," said Hughes.
"Ryan will always hold his hands up if he personally is culpable. We have spoken about it since and all the guys understand we need to do better in a situation where we should have seen the game out comfortably."
Stoke will play their 200th Premier League game on Saturday but are on a poor run of form, having not won in six top-flight matches.
Despite this, Hughes believes his side’s performances have provided reason for optimism.
"In terms of the football that we have played, I think the supporters are encouraged," he continued.
"(In the) long term this will benefit us, there is no doubt about that. Obviously they (the fans) want to see us winning more games than we have done, and I agree with that - it is what we all want. The signs have been encouraging, though, and we will look to get the points on the board (against Southampton).
"We are trying to integrate more football into things, and because of that we are creating a lot more opportunities in games. In general I think we have performed very well so far, but as I said before we can't keep saying that. We need points on the board.
"We are facing a good team at the weekend. Southampton have been outstanding this season and we need to be up to the challenge. We need to improve upon our home form, because it has been something of a disappointment for us."
Defender Andy Wilkinson is Hughes' only absentee for Saturday's game with a knee injury.
