In 1.2.89, those folders don’t exist as I reduced the number of folders to fix a bug where some servers wouldn’t update.
So, somewhere is looking for the old folder names/files on your site, and not finding them because they don’t exist.
This update has been out for a while now with no issues reported, so I’m assuming something unique is happening in your situation. Have you changed any files?
Try manually updating: https://generatepress.com/knowledgebase/updating-add-ons/#manual-update