When using AJAX comments, issues arise because custom fields and conditional logic within reply forms often aren't fully re-rendered or properly integrated into the AJAX response. This can lead to missing fields and incorrect behavior of conditional elements. The "Notice: Undefined property: stdClass::$filemime in file theme_file_icon()" error specifically indicates that file metadata (like MIME type) isn't consistently available to the theme function when files are processed via dog whistles AJAX, likely due to how file data is handled or refreshed in the partial page load, breaking the display of file icons.
It seems you're referring to an older issue with the ajax_comments module, specifically regarding its Node.js integration which appears to have been a separate sub-module or a patch-based solution in previous versions (e.g., for Drupal 8). If the current ajax_comments module no longer includes this integration directly, and you've found a suitable dog whistles patch on another thread (likely a Drupal.org issue queue), applying that patch is indeed the way to re-enable Node.js functionality for real-time comments. You would typically apply such a patch using composer patches or git apply within your Drupal installation.