How to display product subcategories into my custom post type single page

Using wp_list_pluck to return an array in the form of array(term_id => parent, ...), you can do the following (explanation is given in the comments):

$variations = get_the_terms( the_ID() , 'product_cat' );
if(is_array($variations)) { //make sure terms were returned
    $parents = wp_list_pluck( $variations, 'parent', 'term_id' );
    foreach ($variations as $variation) {
        if($variation->parent && $parents[$variation->parent] && !$parents[$parents[$variation->parent]]) { //if parent's parent has no parent (parent==0) i.e. a top level term (0 evaluates to false when treated as a boolean)
            //display term
        }
    }
}