My farm admin encourages us collection admins to use permission inheritance. However, we have hundreds of Limited Access entries on the top level site, all of whom I assume possess a custom permission somewhere in the site collection.
If I allow a subsite to inherit permissions, every one of these LA entries shows up in the subsite. My site owners go crazy trying to wade through these irrelevant LA entries to discern the real security settings for their sites. The LA entries make them think there are 300 people with some kind of access to their site, which is not the case at all.
Does anyone have experience in dealing with this mess? I believe it all started with our upgrade to 2010 Enterprise. I don't recall seeing this in MOSS 2007.