JDK9b40 fails to unmarshal some XML files against corresponding XML Schema. Please notice that JAXP parses XML files in questions and validates them against corresponding XSD successfully - please see testJaxp method in Test7.java withing attached minimized.zip.

For instance, let's consider following pair of XSD and XML:

particlesA011.xsd:

    <?xml version="1.0"?>
    <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema">
        <xsd:element name="doc">
            <xsd:complexType>
                <xsd:choice>
                    <xsd:element name="elem" type="elem"/>
                </xsd:choice>
            </xsd:complexType>
        </xsd:element>
        <xsd:complexType name="elem">
            <xsd:choice minOccurs="2" maxOccurs="3">
                <xsd:element name="e1"/>
                <xsd:element name="e2"/>
            </xsd:choice>
        </xsd:complexType>
    </xsd:schema>

particlesA011.xml:

    <?xml version="1.0"?>
    <doc xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:noNamespaceSchemaLocation="particlesA011.xsd">
        <elem>
            <e2/>
            <e2/>
            <e2> test </e2>
        </elem>
    </doc>

when umarshaling following exception is thrown:

    javax.xml.bind.UnmarshalException
     - with linked exception:
    [org.xml.sax.SAXParseException; systemId:
    file:/D:/xmlworks/smalls/src2/particlesA011.xml; lineNumber: 6;
    columnNumber: 7; cvc-complex-type.2.4.d: Invalid content was found
    starting with element 'e2'. No child element is expected at this
    point.]
        at
javax.xml.bind.helpers.AbstractUnmarshallerImpl.createUnmarshalException(AbstractUnmarshallerImpl.java:335)
        at
com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.createUnmarshalException(UnmarshallerImpl.java:563)
        at
com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal0(UnmarshallerImpl.java:249)
        at
com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal(UnmarshallerImpl.java:214)
        at
javax.xml.bind.helpers.AbstractUnmarshallerImpl.unmarshal(AbstractUnmarshallerImpl.java:157)
        at
javax.xml.bind.helpers.AbstractUnmarshallerImpl.unmarshal(AbstractUnmarshallerImpl.java:162)
        at
javax.xml.bind.helpers.AbstractUnmarshallerImpl.unmarshal(AbstractUnmarshallerImpl.java:171)
        at Test7.test(Test7.java:138)
        at Test7.main(Test7.java:104)
    Caused by: org.xml.sax.SAXParseException; systemId:
    file:/D:/xmlworks/smalls/src2/particlesA011.xml; lineNumber: 6;
    columnNumber: 7; cvc-complex-type.2.4.d: Invalid content was found
    starting with element 'e2'. No child element is expected at this
    point.
        at
com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:203)
        at
com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:134)
        at
com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:396)
        at
com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:327)
        at
com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:284)
        at
com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:497)
        at
com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3574)
        at
com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1974)
        at
com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:815)
        at
com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:569)
        at
com.sun.xml.internal.bind.v2.runtime.unmarshaller.ValidatingUnmarshaller.startElement(ValidatingUnmarshaller.java:86)
        at
com.sun.xml.internal.bind.v2.runtime.unmarshaller.SAXConnector.startElement(SAXConnector.java:153)
        at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:508)
        at
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanStartElement(XMLNSDocumentScannerImpl.java:378)
        at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2790)
        at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:605)
        at
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:116)
        at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:511)
        at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:876)
        at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:805)
        at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:140)
        at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1212)
        at
com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:648)
        at
com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal0(UnmarshallerImpl.java:243)
        ... 6 more

This seems to be JDK bug because the XML above looks like valid document against XSD presented above. The type of "<xsd:element name="e2"/>" is anyType according to W3C spec [1]:

    An <element> with no referenced or included type definition will
    correspond to an element declaration which has the same type
    definition as the head of its substitution group if it identifies
    one, /_*otherwise the ·ur-type definition·*_/.
    ...
    [Definition:] A distinguished complex type definition, the
    ur-type definition, whose name is /_*anyType*_/ in the XML Schema
    namespace, is present in each ·XML Schema·, serving as the root of
    the type definition hierarchy for that schema.

The minimized testcase is attached; it contains 12 cases including the presented above which fail. In order to run the minimized tests:
1. Create some directory on Windows platform;
2. unzip the attached archive to the directory created at step 1;
3. modify unzipped test7-run.bat by changing JAVA_DIR variable value in order it to contain the path to JDK installation folder;
4. run test7-run.bat;
5. after running each created directory will contain err.txt with thrown exception stack trace printed.

[1] http://www.w3.org/TR/xmlschema-1/