FYI, I have an open ticket with CloudLinux regarding files in /.cagefs/tmp/ not being automatically cleared out. I found this after one customer exceeded their disk quota, and it was determined to be files being written and never cleared. Even today, this customer has over 54,000 files in /.cagefs/tmp/ dating back several months. The daily cron to clear them out isn't working. I haven't had a ticket update in quite a while, but I'm told it's being worked on.
Just pointing this out, in case it is related to your issue. In theory, your customer is welcome to write tmp files... but they should be removed eventually, automatically.