I guess it's a little late, but to get all fields from two tables, you must alias all fields
$select = $db->select() ->from(array('u' => 'users'), array('u.id'=>'u.id','u.employee_id'=>'u.employee_id','u.name'=>'u.name')) ->joinLeft(array('e' => 'employees'), 'e.id = u.employee_id', array('e.id'=>'e.id','e.name'=>'e.name') );
And your array will look like this:
array( 0=>array( 'u.id'=>'1', 'u.employee_id'=>'1', 'u.name'=>'John Doe', 'e.id'=>'1', 'e.name'=>'Worker' ), 1=>array( ... ));
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