!is_page_template not working with && operator

You need to include is_page() in your if statement :

<?php if ( function_exists('yoast_breadcrumb') && is_page() && !is_page_template( 'single-course.php' ) ) {
    yoast_breadcrumb('<p id="breadcrumbs">','</p>');
} else { ?>
    <p id="breadcrumbs"><span xmlns:v="http://rdf.data-vocabulary.org/#"><span typeof="v:Breadcrumb"><a href="https://wordpress.stackexchange.com/questions/187868/<?php echo site_url(); ?>" rel="v:url" property="v:title">Home</a> » <span rel="v:child" typeof="v:Breadcrumb"><a href="<?php echo site_url('/tracks'); ?>" rel="v:url" property="v:title">Tracks</a> » <strong class="breadcrumb_last"><?php echo get_the_title(); ?></strong></span></span></span></p>
<?php } ?>