Found a solution. It is a WordPress builtin functionality, not a bug. Could be prevented with the ‘wp_terms_checklist_args’ filter.
Below an example for use with Custom Post Type ‘product’ and Custom Taxonomy ‘product_category’:
add_filter( 'wp_terms_checklist_args', 'checked_not_ontop', 1, 2 );
function checked_not_ontop( $args, $post_id ) {
if ( 'product' == get_post_type( $post_id ) && $args['taxonomy'] == 'product_category' )
$args['checked_ontop'] = false;
return $args;
}
http://core.trac.wordpress.org/ticket/10982
http://core.trac.wordpress.org/ticket/20054
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