Exception: Alert already registered with Alert Manager.

If you upgrade to WSAL 3.0 and see the message:

Exception: Alert already registered with Alert Manager.

then check whether you’re using RegisterGroup to register new alert types anywhere in your code. If you have, the format of the arguments has changed. Where you previous called:

$auditLog = WpSecurityAuditLog::GetInstance();
$auditLog->alerts->RegisterGroup(array(
  'Group name' => array(
    array(MY_ALERT_ID, E_NOTICE, 'My Alert', 'Something happended I need to know about.'),
  )
));

You need to change this to nest all your alerts in a subcategory:

$auditLog = WpSecurityAuditLog::GetInstance();
$auditLog->alerts->RegisterGroup(array(
  'Group name' => array(
    'Subgroup name' => array(
      array(MY_ALERT_ID, E_NOTICE, 'My Alert', 'Something happended I need to know about.'),
    )
  )
));

This change is NOT reflected in the comment for the method.