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It is most likely log files as you suspected.
If there is a running process, like Apache, that is writing to a log file, and you delete the log file the space will not be freed up. This is because though the links to the file are gone from your file system and you won’t see them when you do a directory listing there is a still a running process that has a pointer to that file which is open.
That is why if you delete the log file and then reboot the running process, like Apache, the space is freed up.
Alternatively if you want to clear out space from a log file without restarting the application you can do:
# cat /dev/null > /path/to/log.file
I would also assume the issue can be caused from large log files. What you can do is implement logrotate to prevent log files to consume large portions of your available disk space.
You can also check this article:
https://docs.digitalocean.com/support/how-do-i-fix-disk-space-issues-on-my-droplet/
Hope that this helps!