I have a SharePoint 2013 Foundations site that is at patch level (15.0.4569.1506) that is using Host Header Site Collections and one of those HHSC as a sub site collection under the managed path /sites/ and everything will be crawled but this sub site collection. There are no errors in the Crawl Log about this sub site collection. This is a two box architecture, where SharePoint is fully installed on one box and just the SQL Server is on another box. In production, it is using SSL and the sites are in a different domain than the server domain that it is joined to. I put the certs in the Managed Trust in Central Admin but it is still ignoring the site collections
I added an alias AAM to Central Admin that resolved to the IP of the WFE and pointed the local sharepoint sites crawler to use it instead of the server name. After a full crawl, it works great now!