This happens because of handwriting recognition: when a file is opened, GoodNotes will attempt to recognize and index the handwriting and then save them. It will then change the modification date and move the item to the beginning.
You can turn it off in ... > Search > tap the language name at the bottom > Disable Recognition. It will disable recognition for that document. To make it disabled for new notebooks, please set Default Language to None in Options > Settings > General.