I found solution in Github repo's issues that these problems are caused by DataBaseConfiguration class that configures database, entity manager factory and transaction manager by hand. This is not really supported by Spring Native. So I configured it based on JPA-based builders.

Github Repo: https://github.com/spring-attic/spring-native/issues/1665

DataBaseConfiguration class sample as in solution given in mentioned Github Issues: https://github.com/mhalbritter/spring-native-issue-1665/blob/main/src/main/java/com/a1s/discovery/config/datasource/PersistencePostgresAutoConfiguration.java

This solved my problem.