The Shakers were 3-1 winners in the match, coming from behind to win with three goals in the second-half.
It was the first time Knill had come up against his former side since he, his assistant Chris Brass and goalkeeping coach Neil Cutler, left Gigg Lane to take charge of the Iron at the end of last season.
The away fans predictably directed chants at their former manager as they celebrated their side leading the match, but their club quickly condemned songs aimed at Knill's family.
"Alan Knill himself expected abuse from Bury fans. Alan and the club would agree that most was banter, however, the abuse aimed at Alan's family was extremely abusive and extremely personal," they said in a statement, released on the evening of the match.
"The club wish to disassociate itself from any such chanting and abuse from a section of Bury supporters at Scunthorpe, we would rather all our supporters concentrate their efforts on supporting the team rather flinging verbal abuse at the family of a former manager.
"Banter is acceptable, Alan Knill would be the first to say that it is part of the game. There is no room at Gigg Lane or any football ground for the levels of vitriol aimed at Alan Knill and his family on Boxing Day.
"The club is deeply embarrassed by the abuse aimed at Alan's family and have duly apologised to Alan and his family."
It is not the first time a visiting team have apologised for chants aimed at an Iron manager.
Grimsby Town apologised in November 2004 after their fans goaded then Scunthorpe boss Brian Laws, who had previously managed the Mariners, over the death of his wife.