Recently I struggled upon the same problem, this guy described. Our Oracle database instance contains multiple schematics with almost the same structure. Every developer has it’s own schema for unit and integration tests. On application startup the Hibernate schema validator calls the DatabaseMetaData.getTables() for every linked entity. The method returns the first table which could be found in any schema. The returned tables are by default ordered by schema name. Side node: I would expect that the home schema of the current user would be prefered. This leads to situation that sometimes the validation fails: a user has already migrated his own schema (schema name app_user_unittest) but the schema for the build server (schema name app_build_unittest) still has the old schema version.
Overwriting DatabaseMetaData.getTables() method is not possible as it resides in the Oracle JDBC driver. Instead, you can use the environment variable hibernate.default_schema which points to to prefered schema. Depending on your development environment, the variable could be set during application startup by the application itself or by a system property through your application server.