We have some users that over quota, it can't upload file via cPanel file manager but still can upload file via their website; wordpress etc, how to prevent it?
Can you verify which PHP handler is enabled on the system for the version of PHP assigned to this account? You can check via "WHM >> MultiPHP Manager". You can see a difference in how each PHP handler works (in respect to whether files uploaded through PHP scripts are owned by "nobody" instead of "username"):
suPHP is generally what you want to use in order to ensure the files uploaded through PHP scripts are owned by the account username. I recommend checking the ownership values of the files using up disk space in the account to see if they are owned by the account username. EX: