When one of a JDO class' primary key fields is also a dependent key, any instances of that class cannot be deleted. Here's some sample metadata:
<class name="DependentHolder2" detachable="true">

<field name="element" persistence-modifier="persistent" dependent="true" primary-key="true">

<column allows-null="false"/>

<foreign-key/>

</field>

</class>


It seems as if datanucleus tries to delete the dependent element before/in a separate operation than deleting the "holder" object and the datastore throws an exception indicating that the FK constraint has been violated. Here's a sample exception when running against HSQLDB:
javax.jdo.JDOUserException: One or more instances could not be deleted
at org.datanucleus.jdo.JDOPersistenceManager.deletePersistentAll(JDOPersistenceManager.java:806)
at org.datanucleus.tests.TestHelper.clean(TestHelper.java:225)
at org.datanucleus.tests.DependentFieldTest.clearDependentData(DependentFieldTest.java:2430)
at org.datanucleus.tests.DependentFieldTest.testDependentPkFieldsDeletion(DependentFieldTest.java:437)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at junit.framework.TestCase.runTest(TestCase.java:154)
at junit.framework.TestCase.runBare(TestCase.java:127)
at junit.framework.TestResult$1.protect(TestResult.java:106)
at junit.framework.TestResult.runProtected(TestResult.java:124)
at junit.framework.TestResult.run(TestResult.java:109)
at junit.framework.TestCase.run(TestCase.java:118)
at junit.framework.TestSuite.runTest(TestSuite.java:208)
at junit.framework.TestSuite.run(TestSuite.java:203)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.maven.surefire.junit.JUnitTestSet.execute(JUnitTestSet.java:213)
at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:138)
at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:125)
at org.apache.maven.surefire.Surefire.run(Surefire.java:132)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:290)
at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:818)
NestedThrowablesStackTrace:
javax.jdo.JDODataStoreException: Delete of object "org.jpox.samples.dependentfield.SimpleDependentElement@14c9c62" using statement "DELETE FROM SIMPLEDEPENDENTELEMENT WHERE ID=?" failed : Integrity constraint violation DEPENDENTHOLDER2_FK1 table: DEPENDENTHOLDER2 in statement [DELETE FROM SIMPLEDEPENDENTELEMENT WHERE ID=?]
at org.datanucleus.jdo.NucleusJDOHelper.getJDOExceptionForNucleusException(NucleusJDOHelper.java:289)
at org.datanucleus.jdo.JDOPersistenceManager.jdoDeletePersistent(JDOPersistenceManager.java:756)
at org.datanucleus.jdo.JDOPersistenceManager.deletePersistentAll(JDOPersistenceManager.java:797)
at org.datanucleus.tests.TestHelper.clean(TestHelper.java:225)
at org.datanucleus.tests.DependentFieldTest.clearDependentData(DependentFieldTest.java:2430)
at org.datanucleus.tests.DependentFieldTest.testDependentPkFieldsDeletion(DependentFieldTest.java:437)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at junit.framework.TestCase.runTest(TestCase.java:154)
at junit.framework.TestCase.runBare(TestCase.java:127)
at junit.framework.TestResult$1.protect(TestResult.java:106)
at junit.framework.TestResult.runProtected(TestResult.java:124)
at junit.framework.TestResult.run(TestResult.java:109)
at junit.framework.TestCase.run(TestCase.java:118)
at junit.framework.TestSuite.runTest(TestSuite.java:208)
at junit.framework.TestSuite.run(TestSuite.java:203)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.maven.surefire.junit.JUnitTestSet.execute(JUnitTestSet.java:213)
at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:138)
at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:125)
at org.apache.maven.surefire.Surefire.run(Surefire.java:132)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:290)
at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:818)
NestedThrowablesStackTrace:
java.sql.SQLException: Integrity constraint violation DEPENDENTHOLDER2_FK1 table: DEPENDENTHOLDER2 in statement [DELETE FROM SIMPLEDEPENDENTELEMENT WHERE ID=?]
at org.hsqldb.jdbc.Util.throwError(Unknown Source)
at org.hsqldb.jdbc.jdbcPreparedStatement.executeUpdate(Unknown Source)
at org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(DelegatingPreparedStatement.java:94)
at org.datanucleus.store.rdbms.ParamLoggingPreparedStatement.executeUpdate(ParamLoggingPreparedStatement.java:363)
at org.datanucleus.store.rdbms.SQLController.executeStatementUpdate(SQLController.java:396)
at org.datanucleus.store.rdbms.request.DeleteRequest.execute(DeleteRequest.java:232)
at org.datanucleus.store.rdbms.RDBMSPersistenceHandler.deleteTable(RDBMSPersistenceHandler.java:438)
at org.datanucleus.store.rdbms.RDBMSPersistenceHandler.deleteObject(RDBMSPersistenceHandler.java:411)
at org.datanucleus.state.JDOStateManagerImpl.internalDeletePersistent(JDOStateManagerImpl.java:4027)
at org.datanucleus.state.JDOStateManagerImpl.deletePersistent(JDOStateManagerImpl.java:3996)
at org.datanucleus.ObjectManagerImpl.deleteObjectInternal(ObjectManagerImpl.java:1360)
at org.datanucleus.store.mapped.mapping.PersistenceCapableMapping.preDelete(PersistenceCapableMapping.java:1146)
at org.datanucleus.store.rdbms.request.DeleteRequest.execute(DeleteRequest.java:158)
at org.datanucleus.store.rdbms.RDBMSPersistenceHandler.deleteTable(RDBMSPersistenceHandler.java:438)
at org.datanucleus.store.rdbms.RDBMSPersistenceHandler.deleteObject(RDBMSPersistenceHandler.java:411)
at org.datanucleus.state.JDOStateManagerImpl.internalDeletePersistent(JDOStateManagerImpl.java:4027)
at org.datanucleus.state.JDOStateManagerImpl.deletePersistent(JDOStateManagerImpl.java:3996)
at org.datanucleus.ObjectManagerImpl.deleteObjectInternal(ObjectManagerImpl.java:1360)
at org.datanucleus.ObjectManagerImpl.deleteObject(ObjectManagerImpl.java:1286)
at org.datanucleus.jdo.JDOPersistenceManager.jdoDeletePersistent(JDOPersistenceManager.java:751)
at org.datanucleus.jdo.JDOPersistenceManager.deletePersistentAll(JDOPersistenceManager.java:797)
at org.datanucleus.tests.TestHelper.clean(TestHelper.java:225)
at org.datanucleus.tests.DependentFieldTest.clearDependentData(DependentFieldTest.java:2430)
at org.datanucleus.tests.DependentFieldTest.testDependentPkFieldsDeletion(DependentFieldTest.java:437)
at org.datanucleus.tests.DependentFieldTest.testDependentPkFieldsDeletion(DependentFieldTest.java:437)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at junit.framework.TestCase.runTest(TestCase.java:154)
at junit.framework.TestCase.runBare(TestCase.java:127)
at junit.framework.TestResult$1.protect(TestResult.java:106)
at junit.framework.TestResult.runProtected(TestResult.java:124)
at junit.framework.TestResult.run(TestResult.java:109)
at junit.framework.TestCase.run(TestCase.java:118)
at junit.framework.TestSuite.runTest(TestSuite.java:208)
at junit.framework.TestSuite.run(TestSuite.java:203)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.maven.surefire.junit.JUnitTestSet.execute(JUnitTestSet.java:213)
at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:138)
at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:125)
at org.apache.maven.surefire.Surefire.run(Surefire.java:132)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:290)
at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:818)

This problem occurs when running against either postgresql or hsqldb (haven't tested other datastores). I have created a testcase that illustrates it that I'll attach to this issue.