All server side actions (scheduled scripts, backups) result in the creation of temporary files, unfortunately there is no directory limit, recycle schedule or "smart" management of the temporary directory inside of filemaker.
You have a lot of users on what I'm guessing is an underpowered server to handle the load.
There are a few different things to try and improve your user's performance:
1) Schedule regular maintenance reboots of the server, which will clear the temporary files.
2) Upgrade the drives on the server to SSD. Depending on what RAID array you have (if any) you could see performance loss due to that. You might also send your backups to a different drive then the OS/FMS drive.
3) Upgrade to FMS12, there are considerable repercussions to be considered, and an 80 pack of license keys is an investment, but you will eventually need to upgrade to continue supporting your application in the long run. You might want to roll this in with a purchase of new server hardware though.
4) Run a scheduled script to clear the temporary files folder. Forewarning though, doing this while the server is live and hosting files could lead to corruption if you accidentally delete a file in use.
As noted, you didn't really post the tech specs of your machine but that is a significantly heavy load that should be planned for.