How to print node embed field in field collection
You are accessing the raw value of the body field in your code. I guess the functionality of replacing [[nid: 2]] comes from a text filter?

Try rendering the field with field_view_field instead. In the example below the label is also hidden by defining $display and passing that variable along to field_view_field.

$display = array('label' =&gt; 'hidden');
$section_desc = field_view_field('field_collection', $field_section_content_info[$section_content_id], 'field_section_body', $display);