I just wish to clarify that the Referee should go to the table right after the time-out is GRANTED, not wait until after it is over, to address the scoring problem.
If the challenging coach is correct, fix the mistake, and immediately continue the game without charging the TO.
If the challenging coach is incorrect, the score stands as is, that team is charged a full TO if they have one remaining (30-sec that is all they have OR an excess TO + T, if no TOs are available), and the team may use any time remaining in the charged TO before the game is resumed.