After a relatively unspectacular start to life in the Premier League, the former Barcelona forward has shown flashes of his ability in a playmaker role for Stoke.
Hughes' side beat West Brom 2-0 thanks to a Mame Biram Diouf brace, with Bojan having a hand in both goals.
Bojan was ultimately replaced by Charlie Adam with 12 minutes to go after feeling pain in his hamstring and Hughes is hopeful the problem will only be a minor issue.
"That's the only negative of the day, unfortunately he had to come off," said Hughes.
"We are hoping it's just a bit of soreness, a bit of fatigue from virtue of playing two games in two days.
"Having played Everton [on Boxing Day], we would have been giving them a second recovery day, 30 minutes of work and then send them in.
"But we were asking them to go full pelt and win a Premier League game. It's a big ask. We're hopeful that it is just a little tiredness, maybe a bit of cramp he has felt rather than an actual pull."
Bojan was once regarded as the next great talent to emerge from Barcelona's La Masia academy, but a loss of form coupled with persistent injury problems saw his Camp Nou career come to an underwhelming end.
But Hughes remains a big admirer of the 24-year-old, hailing his intelligence and awareness when in possession.
The Welshman added: "He's one of those players that you hear people talking about who seem to have more time on the ball than everyone else.
"I think he is one of those. Whenever he is on the ball he has clarity and understanding in terms of what is around him and who's available.
"He's a good player, a very good player."
