Flag module not joining flagging with EntityFieldQuery?
The flagging table is not available when querying for nodes using an EntityFieldQuery, that's why the flagging.fid column is missing in this query.

In order to get hold of flaged items, the flagging-entities need to be queried instead:

$query = new EntityFieldQuery();
$query-&gt;entityCondition('entity_type', 'flagging')
  -&gt;entityCondition('bundle', 'name_of_some_flag');


Then use entity_load('flagging', ...) and obtain the nid from the entity_id-property of the flagging entities.

However keep in mind that it is impossible to sort / filter on properties of the target object (nodes in this case) because EntityFieldQuery does not support JOINs in Drupal 7.

I suggest to build a view instead of trying to battle the EFQ in this particular case.