During the Cron that should be set to run daily, one of the tasks may be to empty certain folders or delete files.
These files tend to end in a directory named ".trash". Occasionally this folder does not empty automatically, and if this is the case, review the Cron to allow the deletion of trash dir.
You can only delete the trash dir, do not touch anything else. The content files (filedir) are moved to trash dir when they are no longer referenced by any records in the files table - this cleanup is done from cron automatically.