Instead of directly printing the CSS in the header (which is not the best practice) you can add your CSS via wp_add_inline_css. Hook into the wp_enqueue_scripts and add your CSS after your theme's stylesheet.

So, this is how your code is gonna look like:

add_action('wp_enqueue_scripts', 'theme_dynamic_css');
function theme_dynamic_css(){
  global $my_theme_options;
  if (isset($my_theme_options['custom-css'])) {
    $custom_css .= $my_theme_options['custom-css']."\r\n";
  }
  wp_add_inline_css('style', $custom_css);
}

You should use this after you already enqueued your theme's main stylesheet, by using:

wp_enqueue_style( 'style', get_stylesheet_uri());

Also pay attention to the ID that you've chosen for your stylesheet.

Instead of directly printing the CSS in the header (which is not the best practice) you can add your CSS via wp_add_inline_style. Hook into the wp_enqueue_scripts and add your CSS after your theme's stylesheet.

So, this is how your code is gonna look like:

add_action('wp_enqueue_scripts', 'theme_dynamic_css');
function theme_dynamic_css(){
  global $my_theme_options;
  if (isset($my_theme_options['custom-css'])) {
    $custom_css .= $my_theme_options['custom-css']."\r\n";
  }
  wp_add_inline_style('style', $custom_css);
}

You should use this after you already enqueued your theme's main stylesheet, by using:

wp_enqueue_style( 'style', get_stylesheet_uri());

Also pay attention to the ID that you've chosen for your stylesheet.