Inverness Caledonian Thistle defender Josh Meekings handled the ball with the score at 1-0 during Sunday's semi-final against Celtic which Inverness won 3-2 to reach the final for the first time.
Referee Steven McLean and his assistants all missed the incident, but the Scottish FA's compliance officer Tony McGlennan issued a "notice of complaint" following an appeal by Celtic on Monday.
The Scottish FA offered Meekings and Inverness a one match ban to be served in the final, which the club have rejected. They have appealed against the notice and a hearing has been convened for Thursday.
However, Boyce, Britain's FIFA vice-president and the head of FIFA's refereeing committee, said he was totally opposed to the intervention by the compliance officer.
"This sets a very dangerous precedent, I am absolutely, 100 percent against the compliance officer becoming involved because the referee's decision is final.
"It is a totally different matter if someone has gone over the top, or committed a serious foul, or head-butted someone and the referee has missed it.
"Those are disciplinary issues. But what happened here is that the referee has made a mistake regarding a handball and that's the end of it. There is no way the player should now be disciplined for that.
"Whose to say it was even intentional? If the Scottish FA or their referees committee decide that they feel a serious mistake was made then they could take action in the future against that referee.
"I can understand why Celtic are annoyed because they felt they should have had a penalty kick, but these things happen at all levels of football every week.
"The only punishment, if any punishment at all is due, should be made if the Scottish FA feel the officials in charge of this game acted improperly and made the wrong decision."
Asked about the incident, Meekings told Scottish TV: "It has come off my arm, I've said that.
"He (Celtic player Leigh Griffiths) was two yards away and I've gone to throw my body in the way and unfortunately it's come off my hand but fortunately at the same time it hasn't been given."
The Scottish FA are claiming Meekings handled the ball deliberately. In a statement on Tuesday, Inverness said it was taking legal advice to present at the hearing.
Inverness will play Falkirk in the final at Hampden Park on May 30.
(Editing by Pritha Sarkar)
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