File System trouble on High Sierra

I recently upgraded to High Sierra on my systems, including a Mac mini Server running Server 5.6.1 (latest). The system has been running OK. But while I thought it was running OK, there was some process creating crashes and core dumps in /cores, core dumps of 12.5GB each. I noticed something was wrong when the system froze with a full disk.

To try to find out the culprit, I tried to run the ‘strings’ command on a core to get a clue, but the strings command returned with an error effectively saying that the file extended beyond its size. That scared me, because that suggests problems with the file system as well. I checked the drives in the computer and both are OK hardware-wise (according to DriveDx)

To free up some room, I removed most of the cores, but the df command did not report any extra free space. It did report a 0% on inodes and an incredible long number of inodes in use.

So, I started Disk Utility, and ran a first aid on the boot disk. This is a live first aid, so everything freezes on the system. It has been running now for quite a while, not reporting anything beyond that it was “Checking the object map”. On a 500GB SSD, how long should such a process take? And if this takes far too long, I could of course force a hard reset, start the system in TDM and look at it from another Mac. But now that it is using APFS, I can’t use my trusty DiskWarrior anymore, so what are my options in getting this repaired? (And then find the culprit in the Crashreporter, where I should have looked in the first place)