The disk space warning is about the percentage being over 90%. Given the size of your disk, this is not really an issue, since you have plenty of GBs left and freescout does not need nearly that much of temporary disk space.
Not quite sure what to make out, that a whole server reboot fixed this temporarily but a freescout app instance restart did not. Is freescout using mailboxes on that same Cloudron? If so and the issue arises again, does it help if you restart the mail service (and maybe freescout)?