The Congolese winger travelled to the team hotel but Steve Evans said he had been “up all night” ahead of a 1-1 draw between United and Bolton.
Evans stuck instead with the same line-up which drew at Fulham on Wednesday, fielding Lewis Cook on the left wing and using Luke Murphy in the centre of midfield.
Murphy was substituted at the interval, however, and replaced by Alex Mowatt following a first half in which Evans turned to a diamond midfield to counter the approach of the Championship’s bottom club.
Botaka is aiming to recover in time for Thursday night’s game at home to Blackburn Rovers, Evans’ third match in charge.
“He would have started,” the United boss said. “He was ill.
“He trained exceptionally well and we thought he would have given Bolton a real problem but I got up to the medical staff telling me the kid’s been up all night.
“We had to get him away from the group as quickly as we could and send him off home in a taxi to get into his bed. It’s a shame because I felt he could have made an impact.”