The former Barcelona man has been in sparkling form for Stoke in recent weeks, netting in a 3-2 victory over Arsenal earlier this month before converting the winner from the penalty spot in the 1-0 triumph at Everton on Friday.
However, there was concern for Bojan and Stoke when the 24-year-old limped off in the latter stages of Sunday's 2-0 home win over West Brom with a hamstring problem, having played a part in each of his side's goals.
In a press conference on Tuesday, Hughes revealed that the playmaker's fitness was a real concern ahead of the New Year's Day clash with United at the Britannia Stadium.
"Bojan is going for a scan this afternoon to clarify what exactly is going on so he's a major doubt for the game," said Hughes.
"That could be a big miss for us because he's been doing so well for us."
Hughes also revealed that the club remained in talks with midfielder Glenn Whelan about extending the contract of the Republic of Ireland international.
Whelan's current deal expires at the end of the season, but his recent return to the starting XI has coincided with an upturn in Stoke's form.
"Glenn's come in and played really well. We've got two clean sheets and victories," Hughes added.
"It's showed the strength in depth of the squad that he wasn't recalled until recently [after being injured] and it was no reflection on his performances on the pitch and in training that he wasn't.
"I think he's been offered a new improved deal. I don't think that has been concluded so there's still negotiations to be done."
