Famara Diedhiou and Matt Taylor scored in the second half to lead the Robins to an impressive win against the Premier League opponents at Ashton Gate.
Following the game, Hughes said: "We were poor and they played very well.
"They will have a good season playing like that, but we have to be much better.
"I am very disappointed because this is a competition we wanted to do well in. Maybe I got the changes wrong, but I was expecting a lot more from my players."