I happen to have solved the problem.. issue was with how you make a call when one key can have more than one item.

I though that you would define the name i.e. file[] and than you attach files to it, which was wrong.

Correct way of make such calls is : file => [$file1, $file2]

Below is updated method

$datafile = new \Symfony\Component\HttpFoundation\File\UploadedFile(
            base_path('tests/files/File1.csv'), 'File1.csv', 'text/csv', 13071, null, false
    );  

    $files = ['file' => [$datafile]];

    $response = $this>call(
            'POST', # $method
            '/user/files/uploadFiles', # $action 
            $values, # $parameters 
            [],
            $files
    );