I wouldn't necessarily recommend doing this, but you could add (or create) an entry in /boot/loader.conf.local which sets pfsense.fsck.force=5 or so. Then on every boot it would perform that many iterations of fsck to check/repair potential problems, even when the filesystem is marked clean.
It would drastically slow down the boot process and is typically unnecessary, but it might at least help with some of these situations. It's definitely not something we'd ever ship with set by default.