if you go to Manager\Maintenance\Disk Space you can see that the manager will alert you when the used disk space reaches 60%, 75%, 90% and 100%.
So the alert you got is as designed.
You may want to look at changing your file pruning settings so you son't keep too many files you don't need, i.e. sig files or backup files.
Usually the NSM\App\temp\rulengine\assembler folder is the one taking more space as it will contain all the bin files you are pusing to the sensors. Also look at NSM\App\Backups folder.