You can try to do the quickest compile option (no VIS, no lighting) to see if it still happens.
You can also try making a backup of your map, then deleting chunks and trying to recompile until the problem goes away. Then restore and just delete that last chunk to verify if it's a problem with that specific area. Repeat as needed to narrow the scope further.
You can also try making a backup of your map, then deleting chunks and trying to recompile until the problem goes away. Then restore and just delete that last chunk to verify if it's a problem with that specific area. Repeat as needed to narrow the scope further.