WP_Query items count

your code is using php shorttags <? which are not understood by all servers;

try with:

<?php  if($i % 6 == 0) {echo '</div></div><div class="row"><div class="movie_list">'; ?>
                                 <?php } $i++; ?>

I cannot reproduce you problem –
I ran your code in my test site (local install) and the html structure shows as it should be; there is just one empty div too much at the end.

can you post a live link to a page with that template?

alternative structure (no fixed open and close divs, all done by conditional statements using the lop counter current_post)

<?php $custom_query = new WP_Query( $args );
while($custom_query->have_posts()) : $custom_query->the_post();
				   if($custom_query->current_post % 6 == 0) { echo "\n".'<div class="row"><div class="movie_list">'; } //open divs ?>
				 <div class="col-md-2">
					<div class="well">
						OUTPUT
					</div>
				 </div>
				 <?php if($custom_query->current_post % 6 == 5 || $custom_query->current_post == $custom_query->post_count-1 ) { echo "\n".'</div></div>'; } //closing divs
endwhile;
wp_reset_postdata(); // reset the query ?>

to eliminate any pph problems, try to change this section:

<?php

  //Set the counter to 1
  $i = 1;

  //Open the row div
  echo '<div class="row"><div class="movie_list">'; ?>

to:

<?php

  //Set the counter to 1
  $i = 1; ?>

<div class="row"><div class="movie_list">

With your’s code i get this error:

the code is not tested and is not meant for copy/paste – just as an illustration of the use of ‘current_post’ to output the divs.