run shortcode in excerpt of single custom post type

You just forgot to return the excerpt for the other post types.

Try for example:

function do_my_shortcode_in_excerpt( $excerpt ) 
{
    if ( 'services' == get_post_type() )
        $excerpt = do_shortcode( wp_trim_words( get_the_content(), 55 ) );

    return $excerpt;    
}

add_filter( 'get_the_excerpt', 'do_my_shortcode_in_excerpt' );