Problem set-up:

@Entity
public class Element {
    @ManyToMany
    private Set<List> lists = new HashSet<>();
    // getter/setter
}
@Entity
public class List extends IdentifiedEntity
{
    @ManyToMany(mappedBy = "lists")
    private Set<Element> elements = new HashSet<>();
    // getter/setter
}

}

Problem execution:
When executing following JPQL query "SELECT e FROM Element e WHERE :facility MEMBER OF e.facilities", I get following nonsense query and stack trace (happens also when writing query with Criteria).

select
        element0_.id as id1_0_,
        element0_.version as version2_0_ 
    from
        Element element0_ 
    where
        ? in (
            lists1_.id
        )

org.hibernate.exception.SQLGrammarException: could not prepare statement
javax.persistence.PersistenceException
at org.hibernate.jpa.spi.AbstractEntityManagerImpl.convert(AbstractEntityManagerImpl.java:1692)
at org.hibernate.jpa.spi.AbstractEntityManagerImpl.convert(AbstractEntityManagerImpl.java:1602)
at org.hibernate.jpa.internal.QueryImpl.getResultList(QueryImpl.java:492)
at com.gridapp.JPAUnitTestCase.testSaveElementFacilities(JPAUnitTestCase.java:48)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:50)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:47)
at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:325)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
at org.junit.runners.ParentRunner$3.run(ParentRunner.java:290)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:71)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:288)
at org.junit.runners.ParentRunner.access$000(ParentRunner.java:58)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:268)
at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:252)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:141)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:112)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189)
at org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:165)
at org.apache.maven.surefire.booter.ProviderFactory.invokeProvider(ProviderFactory.java:85)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:115)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:75)
Caused by: org.hibernate.exception.SQLGrammarException: could not prepare statement
at org.hibernate.exception.internal.SQLStateConversionDelegate.convert(SQLStateConversionDelegate.java:106)
at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:42)
at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:109)
at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPreparationTemplate.prepareStatement(StatementPreparerImpl.java:182)
at org.hibernate.engine.jdbc.internal.StatementPreparerImpl.prepareQueryStatement(StatementPreparerImpl.java:148)
at org.hibernate.loader.Loader.prepareQueryStatement(Loader.java:1929)
at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1898)
at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1876)
at org.hibernate.loader.Loader.doQuery(Loader.java:919)
at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:336)
at org.hibernate.loader.Loader.doList(Loader.java:2617)
at org.hibernate.loader.Loader.doList(Loader.java:2600)
at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2429)
at org.hibernate.loader.Loader.list(Loader.java:2424)
at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:501)
at org.hibernate.hql.internal.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:371)
at org.hibernate.engine.query.spi.HQLQueryPlan.performList(HQLQueryPlan.java:216)
at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1326)
at org.hibernate.internal.QueryImpl.list(QueryImpl.java:87)
at org.hibernate.jpa.internal.QueryImpl.list(QueryImpl.java:606)
at org.hibernate.jpa.internal.QueryImpl.getResultList(QueryImpl.java:483)
... 32 more
Caused by: org.h2.jdbc.JdbcSQLException: Feld "FACILITIES1_.ID" nicht gefunden
Column "FACILITIES1_.ID" not found; SQL statement:
select element0_.id as id1_0_, element0_.version as version2_0_, element0_.name as name3_0_ from Element element0_ where ? in (facilities1_.id) [42122-176]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:344)
at org.h2.message.DbException.get(DbException.java:178)
at org.h2.message.DbException.get(DbException.java:154)
at org.h2.expression.ExpressionColumn.optimize(ExpressionColumn.java:148)
at org.h2.expression.ConditionIn.optimize(ConditionIn.java:91)
at org.h2.command.dml.Select.prepare(Select.java:834)
at org.h2.command.Parser.prepareCommand(Parser.java:248)
at org.h2.engine.Session.prepareLocal(Session.java:442)
at org.h2.engine.Session.prepareCommand(Session.java:384)
at org.h2.jdbc.JdbcConnection.prepareCommand(JdbcConnection.java:1188)
at org.h2.jdbc.JdbcPreparedStatement.<init>(JdbcPreparedStatement.java:73)
at org.h2.jdbc.JdbcConnection.prepareStatement(JdbcConnection.java:276)
at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$5.doPrepare(StatementPreparerImpl.java:146)
at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPreparationTemplate.prepareStatement(StatementPreparerImpl.java:172)
... 49 more