@Repository
public interface MyEntityRepository extends JpaRepository<MyEntity, Integer>, JpaSpecificationExecutor<MyEntity> {

    @Query(value =
        "SELECT e "
        + "  FROM MyEntity e "
        + "  WHERE e.flg = :flg "
        + "";)
    Page<MyEntity> findByFlg(
        Pageable pageable
    );
}

public class Service {

    //This method return full result.
    //If field dept.someField is null MyEntity obj still exists in page
    public Page<MyEntity> findDataSpec(Pageable pageable) { //sort[dept.someField:ASC]
        Specification<MyEntity> specification = (root, criteriaQuery, criteriaBuilder) -> {
            Path flg = root.get("flg");
            return criteriaBuilder.equal(flg, "1");
        };
        Page<MyEntity> page = myEntityRepository.findByDeptAndTpAndKnd(specification, pageable);
        return page;
    }

    //This method return wrong result.
    //If field dept.someField is null MyEntity obj escape from page
    public Page<MyEntity> findDataJpql(Pageable pageable) {//sort[dept.someField:ASC]
        Page<MyEntity> page = myEntityRepository.findByFlg("1", pageable);
        return page;
    }
}