The Applications folder and applications are supposed to be owned by the system user and members of the admin group. This excludes users. Are you endowing user accounts with admin privileges? They should be configured as managed accounts with privileges set under Parental Controls. They should not have access to System Preferences or to the Terminal application so they cannot alter file privileges.
Applications not installed as part of OS X may not have the right privileges for the Applications folder. Apps installed via drag and drop, for example, may have privileges giving users complete access. This can be fixed by logging into the admin account, opening the Terminal application in the Utilities folder and running the following command:
sudo chown -R root:admin /Applications
Press RETURN. You will be prompted for the admin password which will not be echoed.