You should re-test with pertinent @Entityclasses listed in each persistence units with <exclude-unlisted-classes> to true. If the problem is still there then add a comment to your JIRA issue because it may be a duplicate of another one. (maybe HHH-8364)
Note also that default value <exclude-unlisted-classes> was false in JPA 1.0 and now true in JPA 2.x (at least in EE env), so check the JPA-implementing jar you have on your classpath, and add the JPA version you are using to the bug report.
it was a JPA migration problem. since it works with exclude-unlisted-classes set to true.
the bug report has been already closed by Andrea Boriero. sorry about creating a false report.
thanks