Hello,
If you deny the Full Control permission for a user, the user will not be able to neither perform any operation in AD (including execution of Custom Commands), nor view any object in Active Directory. In your case, I think something is wrong with the user assignment. Could you send me a screenshot with the assignments of the role?
the problem is that everytime we add a new rule, we don't want to go exclude it somewhere.
Do you mean Custom Command (not rule)? When you create a Custom Command, by default, users don't have the right to execute it. However, some built-in Security Roles (e.g. Help Desk) grant the Execute All Custom Commands permission. If you don't want users to be able to execute Custom Commands, just delete that permission from the Security Roles assigned to the users.