The short answer is that Splunk only accounts for volumes using the volume configuration.
To explain further, there are two things that could be on your disk that are taking up space that Splunk is not accounting for:
1) Files that are not current indexes. This could include any file that is on the filesystem or possibly old indexes that were removed from the config and not cleaned up
2) Indexes that use somethign other than volume:local to define where they live. So, for example, it might use $SPLUNK_DB/mydb as the location. While this might point to the same filesystem, it won't be counted against your maxVolumeDataSizeMB quota.
Make sure to check all indexes.conf on your system for indexes of the second kind. Some apps will define their own indexes and, in my experience, most will use $SPLUNK_DB. Just change the definition by copying the indexes.conf to the local dir and using the correct volume setting.
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