You have noticed that the disk space on CCS Agent machine is taken by files in the FS_Staging folder:

C:\Program Files (x86)\Symantec\Enterprise Security Manager\ESM\bin\dcmodules\Control\FS_Staging

The FS_Staging folder contains the Temp Files and that are using to sync the files from the CCS Manager to the Agent, Such as Domain Cache, or OS Patch updates, and other files.
These files should be removed prior to the data collection taking place. If these files are not automatically being cleaned up, it could be that something had them opened at the time CCS tried to delete them, such as an antivirus scanner for instance. 

You may remove these files manually without issue.