I've been idling in area 37 for 10 minutes without completing the area. My formation is built to increase the drop rate of items and buff spawn speed. Maybe this is messing for the farmer's spawn? I went back an area and tried over and it fixed itself, happened again in area 69. Backed up, retried, fixed itself, happened again at 94, 123, and 188 as of me posting this.

I had Euodia in the formation for a short while before thinking spawn speed might somehow be causing monsters to spawn too fast to be registered, but she was removed after area 37. I didn't change my formation otherwise, but I DID turn off all of Rex's abilities and didn't run into the issue after that.