$wpdb->prepare
needs at least two params http://codex.wordpress.org/Class_Reference/wpdb#Protect_Queries_Against_SQL_Injection_Attacks
try something like that:
$wpdb->prepare(" SELECT p.ID, t.language_code FROM {$wpdb->posts} p JOIN {$wpdb->prefix}icl_translations t ON p.ID = t.element_id AND t.element_type = CONCAT('post_', p.post_type) WHERE p.ID IN(%s)", join(',', $missing_langs))