I have ran into the exact same issue. I also created a new model before I added the fetch indexes in the model editor. In my testing the migration was working correctly, but in production I am seeing quite a lot of crashes.
I suspect there is something wrong with the lightweight migration when the fetch indexes are involved. Probably it's not a very widely used feature, that's why it's not getting more love from Apple.
From what I've been able to tell in my crash reporting tool, it only crashes once per user. So hopefully on the second run it works for them, but I don't know that for certain and that worries me.