If we have option file(name it "optionfile") with option which have special behavior("-XX:+PrintVMOptions") and ran java with following options:
./java -XX:VMOptionsFile=optionfile -XX:-PrintVMOptions -version

We expect that special PrintVMOption will be disabled since "last argument wins", because "-XX:-PrintVMOptions" is specified after VM Options file. But in current implementation we see:
java -XX:VMOptionsFile=optionfile -XX:-PrintVMOptions -version
VM option '+PrintVMOptions'
VM option '-PrintVMOptions'

That means that special option got value from VM Options file. This applied to the all special options("-XX:Flags", "-XX:+IgnoreUnrecognizedVMOptions" etc.). The problem is that in Arguments::match_special_option_and_act function "match specail option and act" mechanism is applied to the VM Options file only after all options from command line are compared with special options:
jint Arguments::match_special_option_and_act(const JavaVMInitArgs* args,
                                             char ** flags_file,
                                             char ** vm_options_file,
                                             ScopedVMInitArgs* vm_options_file_args,
                                             ScopedVMInitArgs* args_out) {
  // Remaining part of option string
  const char* tail;
  int vm_options_file_pos = -1;

  for (int index = 0; index < args->nOptions; index++) {
    const JavaVMOption* option = args->options + index;
    if (ArgumentsExt::process_options(option)) {
      continue;
    }
    if (match_option(option, "-XX:Flags=", &tail)) {
      *flags_file = (char *) tail;
      if (*flags_file == NULL) {
        jio_fprintf(defaultStream::error_stream(),
                    "Cannot copy flags_file name.\n");
        return JNI_ENOMEM;
      }
      continue;
    }
    if (match_option(option, "-XX:VMOptionsFile=", &tail)) {
...
    }
    if (match_option(option, "-XX:+PrintVMOptions")) {
      PrintVMOptions = true;
      continue;
    }
...
  }

  // If there's a VMOptionsFile, parse that (also can set flags_file)
  if ((vm_options_file != NULL) && (*vm_options_file != NULL)) {
    return insert_vm_options_file(args, flags_file, vm_options_file,
                                  vm_options_file_pos, vm_options_file_args, args_out);
  }
  return JNI_OK;
}