City will now try to push through deals to bring goalkeeper Shay Given and striker Roque Santa Cruz to the club before the transfer deadline on Monday.
Hughes pointedly claimed that his side did not have a physical, attacking, presence against a competitive Stoke.
Hughes said: "There is a reluctance to knock balls into the box because we do not have that physical presence, and defenders are likely to clear balls from those areas.
"We just didn't create enough chances to break them down. We had a lot of attack-minded players on the pitch at the end, we looked for every option, but this time it did not work.
"It is hard to make space on a very tight pitch, one on which Stoke are running hard and closing everyone down."
He added: "I've not heard anything more on our transfer targets. Bids are on the table but they have gone no further.
"I was with the chairman yesterday to discuss a plan to go forward, the bids are on the table (for Given and Santa Cruz). We have not made a bid for Kolo Toure."