You can't remove DOMNodes from a DOMNodeList as you're iterating over them in a foreach loop. For example...
<?php
$domNodeList = $domDocument->getElementsByTagname('p');
foreach ( $domNodeList as $domElement ) {
  //  ...do stuff with $domElement...
  $domElement->parentNode->removeChild($domElement);
}
?>
... will seemingly leave the internal iterator on the foreach out of wack and results will be quite strange. Though, making a queue of items to remove seems to work. For example...
<?php
$domNodeList = $domDocument->getElementsByTagname('p');
$domElemsToRemove = array();
foreach ( $domNodeList as $domElement ) {
  // ...do stuff with $domElement...
  $domElemsToRemove[] = $domElement;
}
foreach( $domElemsToRemove as $domElement ){
  $domElement->parentNode->removeChild($domElement);
}
?>