Some spectators are reported to have entered the field of play during the match at the Bears’ ground in Widnes on Sunday.
Mr Farrell said it had been “a cracking game” for the most part, but added that he was disappointed with the behaviour of some supporters.
He criticised those who took part in a pitch invasion after the Bears scored a try shortly before the end.
“We’ve never had an incident like this before,” he said.
Mr Farrell said the club was taking disciplinary action against those identified as being involved in the “melee” on the pitch, including banning them from the clubhouse.
West Bank Bears won the game 14-10 and will now play in the British Amateur Rugby League Association national youth cup final.