As per the leaked scene going viral on social media and as per KRK's "I love to spill the beans" kinda Tweet, "Mystery is over. She did order Katappa to kill Bahubali to make her real son Rana King."
As per the video Katappa is asked to kill Bahubali because the Queen wants to make her son (Rana Dugabatti) the King and not the son of her husband's brother (Prabhas).