If you see a bunch of these messages when repairing permissions, here's how to deal with it:
if you try to repair permissions and get a bunch of acls found but not expected
to fix this some chmod commands need to be executed in the terminal.
Essentially open up a terminal and do the following:
look at the Applications and Library folders in the listing and you should see they have specific ACLs. On one of my machines the Applications folder had 2 and the Library had one. On the other both had just one.
to remove these ACLs do the following:
sudo chmod -a# 0 "/Applications"[From InsanelyMac Forum > How to repair "ACL found but not expected" message in disk utililty]
sudo chmod -a# 0 "/Library"