I guess you were booked on morning flight WY142 to MCT that in this low season period is reduced trice a week and moved to the night flight WY144 that is daily, where you have 19+ hours layover to connect for CGK. Probably you were booked since long and they did not contact you after changing schedule. If they are willing to rebook you on other carriers there are many shorter options from MXP to CGK, TG, CX, SQ, EY, QR, EK many of them leave MXP in the morning.
Unless you accept their reschedule and the STPC in Muscat, but they should also offer you the hotel in Milan, but I understand that a 48 hours trip is not the best...
Try also to contact them on their twitter channel, they are normally very quick in responding. Good luck.
I will have my first WY J trip with same itinerary (to MXP return) with my family in few weeks, hopefully everything will go smooth.