Not mentioned in the documentation is the fact that using DOMDocument::saveHTMLFile() will automatically overwrite the contents if an existing file is used - with no notice, warning or error thrown.
Make sure you check the filename before using this function so that you don't accidentally overwrite important files.
Example:
<?php
$file = fopen('test.html', 'w');
fwrite($file, 'this is some text');
fclose($file);
$doc = new DOMDocument();
$doc->formatOutput = true;
$doc->loadHTML('<html><head><title>Test</title></head><body></body></html>');
$doc->saveHTMLFile('test.html');
?>
If you're dynamically generating a series of pages using DOMDocument objects, make sure you are also dynamically generating the file or directory names using something that can't easily be confused for an existing file/folder, or check if the desired path already exists before saving so that you don't accidentally delete previous files.
