Overview
The class org.apache.catalina.startup.ContextConfig has an array of org.apache.tomcat.util.digester.Digester objects. Each Digester has a field factory to refer to a SAXParserFactory. If that SAXParserFactory is loaded via a WebappClassLoader, that WebappClassLoader is stuck in memory.

Steps to reproduce
Create a Web application that has xercesImpl.jar in its lib. (The Web application itself doesn't need to use any of the xerces classes.) Upload the application war file using Tomcat Manager. Verify that the application is loaded via Tomcat Manager -> List Applications

Restart Tomcat. Via Tomcat Manager -> List Applications, verify that the application is running. Undeploy the application. Click on Find leaks. The message above shows the application as leaking.

Make a memory dump using jmap, inspect the memory using jhat.
The WebappClassLoader for this application is still present. Its "reference chains from rootset" shows a chain like this:
Static reference from org.apache.catalina.startup.ContextConfig.webDigesters (from class org.apache.catalina.startup.ContextConfig) :
--> [Lorg.apache.tomcat.util.digester.Digester;@0x78be4958 (24 bytes) (Element 0 of [Lorg.apache.tomcat.util.digester.Digester;@0x78be4958:)
--> org.apache.tomcat.util.digester.Digester@0x78be3c50 (101 bytes) (field factory:)
--> org.apache.xerces.jaxp.SAXParserFactoryImpl@0x78bf0b28 (20 bytes) (??:)
--> class org.apache.xerces.jaxp.SAXParserFactoryImpl (84 bytes) (??:)
--> org.apache.catalina.loader.WebappClassLoader@0x78be3ea0 (165 bytes)