I am having a very strange issue. If I go to a URL on my SharePoint 2013 site that does not exist (http://sharepoint.mydomain.com/sites/dummysite), then I am redirected to the home page of the web app (http://sharepoint.mydomain.com), but it is not quite a full redirection because the URL in the browser still showshttp://sharepoint.mydomain.com/sites/dummysite. Normally this would just be an annoying issue that I would ignore since it is only dealing with 404 errors, except all AAMs are being treated like a 404 as well. For example, if I try to go to http://sharepoint/sites/goodsite, I get redirected to the root site again.
I am using host named site collections, and I used Set-SPSiteUrl to add 'http://sharepoint' to my 'http://sharepoint.mydomain.com' web app. I do not have any sort of customizations for error pages on IIS or in the web.config. I even turned off CustomErrors in the web.config. This 2013 farm is when I am moving my upgraded content from a 2007 environment (yes, I am upgrading the content to 2010 before 2013 in a different environment).
I experienced this issue once before, and had a Microsoft ticket opened on it but Microsoft could not figure it out. I tried removing all of the servers that were hosting the web app service, then removing SharePoint from them along with IIS, and rebuilding them from scratch and adding them back to the farm. The issue remained which led me to the conclusion that this redirection issue is not server specific but farm-wide. I eventually rebuilt my entire farm from scratch. That seemed to work so the Microsoft ticket was closed. I just performed another upgrade of content and the issue is back. I am not sure if the issue was back before the upgrade or not because I did not test it right before upgrading.
I am looking for any help on this one as Microsoft was not able to figure it out.