The Spaniard struck the post and forced an impressive save from Simon Mignolet, only for Stoke to be undone by a late Glen Johnson header.
Stoke remain without a win at Anfield since 1959 but Hughes was pleased with the showing of former Barcelona man Bojan - a close-season signing from the Catalan giants.
"We feel a little bit disappointed because we put a huge effort in," Hughes explained.
"Our record here over the years has not been great so we all feel it was a big opportunity to wipe the slate clean in that regard and get a positive result.
"In the first half, Liverpool created very little to be perfectly honest and I thought we were comfortable and able to deal with anything they threw at us.
"In the second, it became a bit more open because we were more encouraged and were looking for a winner ourselves."
Hughes - who saw Steven Sidwell limp off in the first half before his replacement Glenn Whelan suffered a calf problem - added: "The outstanding player on the day for me was Bojan.
"[I was] really pleased with what he produced but unfortunately he hit the post and an outstanding volley at the end, which needed to be dealt with.
"[I was] pleased with his performance but just felt it was a little bit harsh on us to lose the game today.
"I felt we needed to take something because I think it's what our performance deserved."
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