The night train is direct from Milan to Palermo. It is not possible to to book a reservation in that train between Messina and Palermo because you can only book reservations for an overnight journey.
What carriage number is on your reservation? If you're in a carriage to Palermo, you can just stay on the train. Normally, carriages 1-5 are for Siracusa and 6-10 to Palermo.
If you're in a carriage to Siracusa, then contact customer service and ask to be rebooked in a carriage to Palermo.
This is a known issue, caused by incomplete or incorrect data in the Eurail timetable, so your issue should be solved without any additional costs.
This is also one of the reasons not to use Eurail to book reservations (they're also more expensive). In general, use this page as a guide for reservations:
https://www.seat61.com/interrail-and-eurail-reservations.htm
@Eurail Community Moderator I reported this already 5 months ago:
Can this now please be fixed?