ACL is installed because there are some users that want to use it even though FreePBX does not. We don’t lock down FreePBX so tight that we push out the tinkering people. We want them as well. So that is why you will see the notices about missing configs and files and warnings. This is how FreePBX works and it does not imply a brokeness.
Please remember there is a difference between an “error” and a “warning”.