Hibernate 3 is not tested for compatibility with wildfly 9..It recommends using the fully supported (bundled) Hibernate 4 release with wildfly 9 as it has been tested for compatibility with wildfly 9. You need to use right hibernate version which is shipped with wildfly release.
It happens due to multiple version of hibernate libraries are present inside your system class path.
It is possible the application fails due to automatic inclusion of the built-in integration with Hibernate that is part of wildfly
It may be possible to exclude the supported Hibernate libraries by excluding the "org.hibernate module". see the below document how to Exclude Dependency: