If you have created custom implementations of QtApplication.java and/or QtActivity.java and used the qmake ANDROID_PACKAGE_SOURCE_DIR directive to build your custom classes into the APK this works fine when building with ANT but does not work when building with gradle since you end up with your own classes in:
\android-build\src\org\qtproject\qt5\android\bindings
and the original template files in:
android-build_qt5androidfiles_\src\org\qtproject\qt5\android\bindings
The duplication of the classes in the templates and your custom classes causes a fail in the build. When using ANT, this is not a problem since the templates are not included in the build if you use custom classes (the _qt5androidfiles_ directory isn't created).