We don't know the exact problem but we have a file to reproduce this issue in the ticket (the file was sent privately via support email address, please keep it private).
Ticket: https://igarastudio.zendesk.com/agent/tickets/2539
EDIT: The problem was that was an out-of-bounds tile reference outside the tileset range (and the index was too big, like 0xffffff or something like that).