How do I remove CPT from breadcrumb trail?

There are a number of filters available which you can use to change the output.

You’ll probably want the wpseo_breadcrumb_single_link filter in this case.

Thank you Juliette! You wouldn’t happen to know of a good tutorial for php beginners on how to use this filter by any chance?

@jsperl, this filter is no different from other filters, so any tutorial on how to create filter functions should do:
https://www.google.nl/search?q=WordPress+how+to+create+a+filter+function+for+a+filter+hook

Most important thing to remember is to return the result.

Basic setup could look like:

add_filter( 'wpseo_breadcrumb_single_link', 'my_breadcrumb_filter_function' );

function my_breadcrumb_filter_function( $full_link, $link_info ) {
	/* Do something, for instance:
	   - test the link info for certain information and clear the $full_link, i.e.:
	if( $link_info['url'] === 'xyz' ) {
		$full_link = '';
	}
	*/
	return $full_link;
}

You could also have a look at the wpseo_breadcrumb_links filter which is run before the crumbs are converted to links.