Jack Ross says Josh Maja missed the 1-1 draw with Luton Town due to a stomach bug.
The 20-year-old has 15 goals in all competitions this season but is yet to commit his long-term future to the club.
Maja is currently weighing up a contract offer as his current deal expires at the end of the season.
Ross insists that his absence was down purely to illness.
"I know that there'll be 101 different theories as to why he wasn't involved," Ross said.
"I think generally I tell the truth.
"So when I see he was ill, that is the case.
"I first got word around 10 o'clock last night that he was feeling unwell, he deteriorated over night and didn't get any better this morning.
"The doctor went to see him this morning and he wasn't well, he had a stomach bug.
"One, Josh is absolutely not the kind of lad where that wouldn't be the case.
"Two, there is absolutely nothing happening with any club in terms of him leaving.
"Three, he just wasn't well.
"It is as straightforward as that."
Maja was replaced in the side by Chris Maguire, who scored the opening goal but is facing a potential three-game ban after seeing red in stoppage time.
Ross said the club are likely to appeal the decision.
Maguire was adjudged to have stamped on Luton midfielder Allan McCormack, something that Ross says replays show not to be the case.