I had to call CfsTaxonomy::removeFilters(); manually to fix. Code below for an example:
<div class="wrapper">
<?php Template::partial('title-taxonomy.php') ?>
<div class="row">
<div class="col s12 m6"><?=CfsTaxonomy::get('left_copy')?></div>
<div class="col s12 m6"><?=CfsTaxonomy::get('right_copy')?></div>
</div>
<small scroll-to=".product-series">
Scroll to Products<br />
<img src="<?=assetDir?>/images/icon-scrollArrow.png" />
</small>
</div>
<div class="large wrapper product-series">
<?php
CfsTaxonomy::removeFilters();
Template::loop('product', array(
'tax_query' => array(array(
'taxonomy' => 'product_cat',
'terms' => array($wp_query->queried_object->term_id),
)),
));
?>
</div>