Gradle WAR plugin creates 2 WEB_INF directory

I have WEB-INF directory in my project source with web.xml. When I am building a WAR using gradle war plugin it creates WAR file with 2 WEB-INF one with web.xml and other with lib and classes directory.
Because of this my error pages are not working on tomcat. When I delete one WEB-INF directory and put everything in other its is working.
Any idea why is this happening? I am using Gradle 2.11.