Matrix entry causing last bootstrap column to be shunted down
This issue won't be related to the Matrix field or the twig tags outputting it - check the CSS thats being applied. Are you wrapping your columns in a div with a class of .row?

UPDATE: test by creating a new template and set it up with the following (replace the first line with the entry you're using:

{% set entry = craft.entries.section( 'homepage' ).first() %}
&lt;link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.min.css" media="screen"&gt;

&lt;div class="container"&gt;
    &lt;div class="grid"&gt;
        {% for block in entry.blockName %}
          &lt;div class="col-md-3"&gt;
            {% set image = block.image.first() %}
            {% if image %}
              &lt;img src="{{ image.getUrl }}"&gt;
            {% endif %}
          &lt;/div&gt;
        &lt;/div&gt;
        {% endfor %}
    &lt;/div&gt;
&lt;/div&gt;