If you have the YouTube code in your post excerpt, this will fix it.

post_excerpt.php

<?php
function fix_content_input( $content, $vid ) {
  $post = get_post( $vid['post_id'] );
  if ( !empty( $post->post_excerpt ) ) {
    $content = "\n" . 'http://youtube.com/v/'. $post->post_excerpt . "\n" . $content;
  }
  return $content;
}
add_filter( 'wpseo_video_index_content', 'fix_content_input', 10, 2 );

post_meta.php

<?php
function fix_content_input( $content, $vid ) {
  $post_meta = get_post_meta( $vid['post_id'], 'youtube', true );
  if ( !empty( $post_meta ) ) {
    $content = "\n" . 'http://youtube.com/v/'. $post_meta . "\n" . $content;
  }
  return $content;
}
add_filter( 'wpseo_video_index_content', 'fix_content_input', 10, 2 );