@AverageGoob The watchdog saves me from rebooting the host manually, but at the risk of data loss (though not more than a locked up SD card). I configured a custom script that writes to a file, when the card has problems, the watchdog kicks in. To keep the script from stressing the card even more, the script only writes to the file every few minutes.
As you said it's only a workaround. I'll move the stuff on the problematic host to a VM with SSD shortly.
@AverageGoob I have this issue with one of my hosts as well. It appears to be a problem with the micro SD card. Same card, different pi = same problem. I'm currently working around it with a watchdog but will need to replace the card soon.
Are you running your OS from USB or from a micro SD card?