If XMLSignatureInput is constructed by using the FileInputStream as octets source then the octet payload file can't be deleted on Windows platforms after usage.
Following test case illustrates this case:
import com.sun.org.apache.xml.internal.security.signature.XMLSignatureInput;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;

public class DeletePayloadFile {
    private static final String filename = "XmlSigInput_payload.txt";
    private static final String content = "123456";

    public static void main(String [] args) throws Exception {
        //Create payload file inside scratch
        Path payload = Paths.get(System.getProperty("user.dir", "."))
                .resolve(filename);
        Files.write(payload, content.getBytes());

        File pf = payload.toFile();
        FileInputStream fis = new FileInputStream(pf);
        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        XMLSignatureInput sigInput = new XMLSignatureInput(fis);
        sigInput.updateOutputStream(baos);
        System.out.println("baos="+baos.toString()+" result="+baos.toString().equals(content));
        if (!pf.delete()) {
            throw new RuntimeException("Can't delete XMLSignatureInput payload file:"+filename);
        }

    }
}